The problem is a bit Lower than Charles' Head
Yeah pretty much. Suddenly being crowned King of Burgundy/Lothringia is not going to change the fact that Charles' only child is still Mary of Burgundy.
You could possibly get it to make Charles less Bold and thus say it gets him to survive longer, which may give him time to sire a Son, but that isn't Guaranteed and honestly, if 20+ some odd years wasn't enough time, I doubt a few more would help much. Charles, although he died in battle, was 44, it wasn't like he was some rambunctious 20 something cut down before he had a chance to shine.
Without resolving the lack of a male heir, all you've done is give the Hapsburgs yet one more Royal Crown to add to their collection.
ADDENDUM: What it could do, which would be an interesting direction to take this PoD, is get the Division of the Hapsburg Territories to change. Alternatively, if the Maximilian-Mary Marriage is recognized earlier, you might give Max and Mary a stronger position, so they might keep more of the Burgundian Territories.