The Treaty of Berlin (1878-9) allowed for the occupation and administration of Bosnia/HG only to the extent that it did not abrogate the personal rights of the sultan in the territory. The language included the statement (in French) reading:
The fact of the occupation of Bosnia-Herzegovina does not prejudice
[ne portant pas atteinte] the rights of sovereignty of H.S.M. the
Sultan over these provinces.
Although technically the Sultan had all kinds of personal rights, in practice very few of these were actually exercised during the occupation, the main one being the raising of the Ottoman crescent flag over every mosque during the hours of prayer. Technically, the Sultan was entitled to a range of other various rights such as taxation monies and to arrest and execute anyone who insulted or criticized him, among other things; but these rights were ignored after the Austrians took power.
According to the London Convention of 1871 there was an agreement that the convening powers (including England and Austria) would not break any of their treaties without the consent of the others.
Another key factor was that the takeover of Bosnia was controversial in Austria because it required a large number of troops and involved fighting. Due to the controversy, there was enacted a law in 1880 that explicitly blocked Bosnia from being adducted to the monarchy except by the vote of both parliaments of Austria. This alone prevented Bosnia from being annexed to the monarchy for a long time, even though Austria ruled Bosnia de facto.
The political situation changed in 1907-8. Firstly, the Serbs began supplying weapons to Bosnia and agitating by setting off bombs. Several newspapers in Sarejevo began publishing pro-Ottoman editorials, saying things like they only had fealty to the Sultan and so forth. Since Bosnia was ruled by a provincial diet, not the emperor, there was nothing directly the monarchy could do about this.
Simultaneously, the gears began to turn. The Bulgarians wanted to seize Macedonia and the Austrian monarchy wanted to help them. To do this they began building a military train line called the Novi Bazar line out of Bosnia into Macedonia. This move would be guaranteed to activate pro-Ottoman revolutionary activity in Serbia and Bosnia, so the monarchy began to plan for an annexation so they could get dictatorial powers in Bosnia and not have to go through the provincial diet. When the Bulgarians declared independence it invalidated the Treaty of Berlin, so the monarchy felt that "legally speaking" they no longer had to respect the sovereignty of the sultan so they annexed Bosnia two days later and got rid of the provincial diet.
To answer your main question, the main autonomy the Bosnians lost by the annexation was that laws were no longer made by the provincial diet, but rather by the crown of Austria.
