Hi Craig,
If you follow the family in the censuses, you will find they are all still Bullions in the 1841 and 1851 censuses, but by 1861 most of the family seem to be listed on the census as Bunyans. The marriage entry for Francis's brother James in 1847 does appear to be under Bunyan though. I don't think that John Bullion and Elizabeth Forbes named their children Bunyan, I think it was just a gradual shift over time due to accents/dialect and reliance on others to write down names.
Francis was indeed the son of John Bullion b. 1793 d. 1855. Death entry under Bullion but gravestone Bunyan. However I've never definitively got the line any further back than that. Would be great to learn more about the Glenalmond link.