According to Draper the relative that Squire Jr. apprenticed with was his cousin Samuel. By the time Squire Jr.'s family met up with him again (they had temporarily removed from western NC during the late part of the F&I War) - around the late 1750s-1760 period, Samuel was working in Maryland near Georgetown, present DC. Some accounts say Squire worked with him for up to 5 years. Samuel made gunlocks on military contracts during the Rev. War and ended up going broke, and then joined his family in Kentucky in the late 1780s. He spent some time making and repairing guns for the Chickasaw near Natchez. Unfortunately, no surving guns by his hand have surfaced.
So you have a family with ties to the Reading, PA area, that moved down the Great Wagon Road to western North Carolina before the F&I War, with some members being trained in gunsmithing in Marlyand and possibly Philadelphia prior to that - then moving back to Rowan County North Carolina. So with regard to rifles, really any of them could have been carrying a rifle from just about from any region between eastern PA and the Carolina piedmont. I would suspect that even in the cases of his rifles that were not lost, Daniel Boone's lifestyle would have been pretty hard on a rifle so I would also suspect that he was probably not carrying anything extremely old when first ventured toward Kentucly in the late 1760s. Going with that line of thought, something either made by his brother or from a gunsmith from right around where he was living at the time - the Yadkin region - Rowan County or neary areas, would be as good a bet as any. There were lots of gunmakers working in Salisbury by the 1770s.