The word 'Galldachd' for the lowlands arises from the Old Irish 'gall' for 'foreigner' which came in turn from the Latin word 'gallus' for a Gaul. http://www.wordsense.eu/Gall/#Old_Irish.
The Gaels called (indeed call) their linguistically and culturally Gaelic part of Scotland the Gàidhealtachd, usually translated as 'Gaeldom'. This cultural way of viewing the world gives a hint to what the Gaels meant when they said 'foreigners' ... they basically meant 'land of the non Gaels'. 'Foreigners' was not meant necessarily as any sort of denigration - it was just a simple statement of cultural and linguistic fact.
The Irish word 'galldacht' has a closely related sense (although not identical) of the English, English speakers and the region of the Irish Pale, and therefore 'Galldachd' also had or came to have a sense of 'a region that is culturally English' - again meant as a simple reflection of the shared language and culture of lowland Scotland and England at that time, and not as any kind of denigration or diminution of Scottishness.
In the years when these terms developed, there was no nation of Scotland, and Gaelic Scotland had little in common with the part of modern Scotland where people spoke the precursor dialects of Middle Scots. Even after the political entity of Scotland came into existence, the highlands and islands remained strongly distinct, and weakly controlled by the lowland Scots monarchy. A long tradition of antipathy between the two cultural regions meant that there would have been little motivation to ever stop calling the lowlands by a word that tended to underline the separation between the peoples.