Ming -> Qing isn't like Valois -> Bourbon, but more like Navarra -> France as far as I understand.
The change from Valois to Bourbon dynasty is entirely different from Ming to Qing. It was just that the king of Navarra got a PU over France, as the rightful heir to the crown of Henri III.
The Ming to Qing change is simply that the united Jurchen tribes conquered the collapsing realm of Ming, and crowned themselves emperor after having conquered the most important parts of it. This game is actually centered around Europe, and therefore one should not be surprised that it cannot portray at the same level of coorrectness completely different worlds, and prefering to portray Europe the best.
Why not just apply this logic to the east?
The problem here is only half the inability of the Qing to form, and the other half is that if Ming is not absurdly nerfed with completely absurd penalties that make absolutely no sense whatsoever... it is a complete monster who dominates the region.
That's the real issue here. Qing defeating and absorbing the Ming? EASILY handled with an event or decision, that would allow this conglomeration after uniting the tribal area and controlling Beijing or whatever criteria. It could follow a similar route to the Burgundian inheritance but would be Ming inheritance, or it could follow a more Polish route and allow the Ming player to pull the Manchu in but retain "ownership" of this new PLC-like Qing even though it's technically the Manchu leader, much like Poland grab's Lith's leader but is PU major. It could be something else. This only resolves half the problem.
If they did this, while fixing the whole Qing formation, we are left with the game's truly glaring problem, which has always been a problem, and that is that the game does not make any modicum of an effort to balance oversize empires, overextension other than "coring" system, etc. Throw Ming/China in at 1444 with the same routine government and Chinese tech of any neighbor, and suddenly you have an unstoppable and uncontainable power in the east that cannot fail, because there's no containing force like France etc have nearby.
So, at the end of it all, it's really not about Qing so much as its about a complete lack of balance of power or diminishing returns on size, so Ming are just TOO GOOD for the 1444 game.