It is weird, that you must do some quest, join faction or even buy house to get all Stones of Barenziah. This is roleplaying game, so game should't force you to do it. 

I moved locations of three Barenziah Stones to near orginal places. WARNING! contain spoilers of four stones locations 

Stone from Dark Brotherhood sanctuary is moved to Jarl's house in Falkreath 
Stone from Arc Mages quarter is moved to jarl's house in Winterhold 
Stone from buyable house Proudspire Manor is moved to Bard's College 

Stone in Thalmor Embassy is already moved by Unofficial Skyrim Special Edition Patch to cave under Embassy, so I didn't