Margaret, Duchess of Burgundy, was a Yorkist through and through. If she has a son, he is marrying one of her nieces, there's not a doubt in my mind about that. And she will be supporting her young nephew's claim to the throne. Look how strident she was in supporting Perkin Warbeck, and Edward of Westminster is her undisputed nephew, she's going to redouble her efforts if its for him. Of course, this assumes they get out of the Tower and out of the country, which is no guarantee.
If the POD is a Lancastrian Victory at Barnet, then yes, Edward of Lancaster and Anne Neville are going to be the next King and Queen. Indeed, I could see Edward being made Regent for his father, if Henry's health stays as bad as it was OTL. One possibility for a peace-making match, if the Yorkist children aren't smuggled abroad, would be OTL's Edward V to the eldest daughter of Edward of Lancaster and Anne Neville, as long as the age gap isn't completely unworkable.
What fascinates me would be how the Nevilles are viewed in this AU. Warwick would be a Kingmaker twice over and the father-in-law of the next in line, assuming he survives Barnet, so you'd expect him to be rewarded. At the same time, however, his other daughter is married to George of Clarence, the younger brother to the Yorkist Usurper, whose loyalties are only ever going to be in question. That in turn, may well reflect on Warwick...