The quick answer (If there is one) is that Simon didn't control those churches(which were essentially the homes/estates of secular canons), he just set aside and funded the construction of the new home (Newenham) for the existing secular canons which were already associated with the church of St. Paul's.
This was taking place as a conversion of secular to regular canons agreed upon by both the church and the monarchy, due to some controversy at the time.
From A brief History of St. Paul's
The conduct of the clergy in Bedford does not seem to have been as
exemplary as it ought to have been, however, and in 1164 one of their
number, Philip de Broy, killed a man, and, whatever the circumstances
were, it damaged the good name of the canons of St Paul's. This
situation was not uncommon in other towns at the time, and in order to
avoid such incidents several other collegiate foundations had adopted
the practice of housing such clerics together in priories following
the Rule of St Augustine.
This was seen as a satisfactory solution for Bedford, and the countess
of Bedford Castle, Rose de Beauchamp, and her son Simon, found a
suitable site just outside the town. In 1165 at a service in St
Paul's, Simon confirmed that all the canons prebends and possessions
be transferred to a spot about a mile downstream of Bedford, which
they named "Newenham" or "new home" - now known as Newnham.
This essentially converted the secular canons of the collegiate church to regular canons of the Augustine priory. The wiki article on canons clarifies the difference somewhat:
Originally, a canon was a cleric living with others in a clergy house
or, later, in one of the houses within the precinct of or close to a
cathedral or other major church and conducting his life according to
the customary discipline or rules of the church. This way of life grew
common (and is first documented) in the eighth century. In the
eleventh century, some churches required clergy thus living together
to adopt the rule first proposed by Saint Augustine that they renounce
private wealth. Those who embraced this change were known as
Augustinians or Canons Regular, whilst those who did not were known as
secular canons.
The History of the County of Bedford discusses the establishment of the Priory, and the assets it controlled (emphasis mine):
The original endowment of the priory by Simon de Beauchamp comprised
the tithes of fourteen churches—St. Paul's Bedford, Renhold,
Ravensden, Great Barford, Willington, Cardington, Southill, (fn. 34)
Hatley, Wootton, Stagsden, Lower Gravenhurst, Aspley, Salford,
Goldington; portions of land in many places which had belonged to the
old canons; the tithes of all his markets, assarts and woods; the
castle mill and another with some lands and water attached; the free
use of all waters belonging to the castle, as far as Fenlake, for
fishing, navigation and breeding swans; and the right to pasture a
certain number of cattle with his own free of cost. These gifts are
rehearsed with much detail and some additions in the Great Charter of
William de Beauchamp. At the time of the Taxatio the income of the
priory appears as £164 10s. 8d., (fn. 35) of which £92 6s. 8d. is made
up of spiritualities. The largest items amongst the temporalities are
lands, etc., at Goldington, Salpho, Stotfold and Sharnbrook; (fn. 36)
and these are found in the Feudal Aids as portions of knights' fees.
This information is repeated in the book Money and the Church in Medieval Europe, 1000-1200: Practice, Morality and Thought
...the estates of the pre-existing secular canons were transferred to
the new house, along with the tithes of 14 churches in Bedfordshire...
So this clarifies the issue and the distinction between the two groups of 'churches' mentioned. Those that were in the possession of the secular canons went with them into the priory, to be absorbed (depending on each of those original deeds) into the priory's funds when these canons passed.
This is mentioned directly in another source, The Schools of Medieval England, by Arthur Leach:
the Norman lord Simon Beauchamp founded in Bedford an Augustinian
priory and provided that as the secular canons of St Paul's died off
they were to be replaced by regular canons and granted the church to
them One of the secular canons was Nicholas also Archdeacon of Bedford
and Canon of Lincoln About 1155 he executed a deed clearly under
compulsion addressed to 'all the sons of holy mother church' Know ye all
that St Mary's chapel with the tithes of Hordelhide and Bedford school
scolas Bed which I have held for some time with the consent of my
fellow canons I confess to be of the right of and appurtenant to St
Paul's church and therefore I have voluntarily resigned them to Auger
the Prior and the convent of canons regular of that church The priory
having acquired the church and school was afterwards moved outside the
town down the river to Newenham and became known as Newnham Priory Not
till after the dissolution of monasteries did the school escape from
the control of the regulars when it was refounded by the corporation
under a charter of Edward VI and re endowed by William Harper ex Lord
Mayor of London under Queen Elizabeth
Another document from the same Cartulary provides insight into the others involved in this decision/transaction; the authority by which these transfers were made.
Charter document 7 from the Deeds collection of the University of Toronto
Simon de Bellocampo omnibus fidelibus sancte ecclesie salutem Notum
sit vobis quod ego Symon de Bellocampo dedi et firmiter concessi
ecclesiam sancti Pauli Bed[] cum omnibus prebendis et possessionibus
eidem ecclesie pertinentibus ad religionem in manus Willelmi primi
prioris ibidem canonice constituti et in manus omnium successorum eius
professionem religionis tenencium pro salute anime mee et pro anima
patris mei et omnium antecessorum meorum qui supradictas prebendas de
suis elemosinis ad seruiendum deo fecerunt et pro salute anime matris
mee comitisse Rohesie et fratrum meorum et omnium parentum meorum Si
vero prior decesserit electione conuentus et meo assensu alius prior
substituatur Hanc donacionem confirmari feci auctoritate apostolica et
domini mei Henrici regis Angl[] assensu et confirmacione annuentibus
Thoma archiepiscopo Cant[] et Roberto Linc[] episcopo Hec autem
donacio sollempniter facta est in supradicta ecclesia sancti Pauli
astante clero et populo Huius donacionis et confirmacionis mee sunt
testes Albricus comes auunculus meus Willelmus comes frater meus
Rogerus Bigod Gilbertus de Ver[] Galfridus Loring[] Paganus filius
Brien Radulphus de Berner[] Walterus de Mand[] Hosbertus filius
Ricardi Reginaldus de Auco Willelmus de Bouill[] Johannes de Rochell[]
Robertus de sancto Quintino Radulphus Folenfaunt Rogerus filius
Huberti Radulphus clericus
this roughly translates:
Simon de Beauchamp, to all the faithful of the holy church, let it be
known to you that I gave and firmly granted the church of St. Paul
Bede, with all prebends and possessions belonging to that church, into
the hands of William the first prior, canonically placed there and in
the hands of all his successors. a profession of religion that hold
fast for the safety of my soul and for the soul of my father and of
all my ancestors who have made the above-mentioned prebends of their
alms to serve God another prior to be substituted I made this gift
to be confirmed by the apostolic authority of my lord Henry king of
England and with the assent and assent of Archbishop Thomas of Cant
and Robert Linc Bishop Witnesses to my confirmation are Earl Aubrey,
my uncle William, Earl my brother Roger Bigod, Gilbert de Ver,
Geoffrey Loring Payne, Ralph de Berner, Walter de Mand, Hosbert son of
Richard, Reginald de Auco, William de Bouill, John de Rochell []
Robert of St. Quintinus, Ralph of Folenfaunt, Roger the son of Hubert,
Ralph, clerk
We can see that this transaction was not just by Simons authority alone, but listed Bishop, Archbishop and King as backing the deal...
(Its worth noting also that this archbishop mentioned was Thomas Becket, and that Simon Beauchamp is listed as one of the signers of the Constitutions of Clarendon in 1164)
An explanation of the term prebend, and its relationship to the secular canons may help clarify this issue as well:
At the time of the Domesday Book in 1086, the canons and dignitaries
of the cathedrals of England were supported by the produce and other
profits from the cathedral estates.3 In the early 12th century, the
endowed prebend was developed as an institution, in possession of
which a cathedral official had a fixed and independent income. This
made the cathedral canons independent of the bishop, and created posts
that attracted the younger sons of the nobility.
So by by creating a powerful priory such as this, the Church consolidated its wealth and control, while the Monarchy removed a loophole through which lesser nobles were removing lands from the kings control and essentially providing inheritance to younger sons by establishing them as secular canons.
No more 'loose canons' so to speak.