Charles the Bold is already married to a woman who wouldn't die until 1503. Again, this isn't just a "Survive=Have Son" situation. Charles is 44. He's not some strapping young lad who was cut down before he had a chance to make a family. He's not Young, and neither is his Wife, she's 31.
Assuming he does manage to father a son with Margaret that if anything puts him closer to the English Throne, but there's still a million things that could keep his descendants from getting either the throne of France or of England. If Burgundy's relations with either are poor, and they'll almost assuredly be poor with one or both, they'll laugh in its face and choose someone else.
If a Duke of Burgundy does become King of France then they're unlikely to keep many of their non-French Holdings while the Duchy of Burgundy itself will probably just become another Duchy in the Kingdom of France. If the Dutch have not already rebelled they'll do it then with Imperial and English support at the very least, Spain will probably also get involved because none of them will want such a massive France to exist. You'll see a "War of Burgundian Succession" similar to the "War of Spanish Succession" except France will probably be in a weaker situation.
I expect in that situation the Netherlands will either become independent or, depending on the religious situation, may be ruled by The Emperor, seized via the Imperial Ban. Most likely I think you'll see a big Netherlands that is friendly to and part of The Empire while the French lands of Burgundy are absorbed into France itself.
True, of course, Charles, looking towards the future, could always have the Pope annul marriage if he wanted to secure his line. Assuming he did that..
And his descendants still rule Burgundy, the French chose the Duke of Burgundy. After all, they chose a Protestant King of Navarre as king even if he was, by Salic Law, incredibly distant. How many degrees was Henry IV related to Henry III in the male line? A surviving House of Burgundy would undoubtedly be chosen as long as they are Catholic, and when the Duke of Burgundy become the heir presumptive, he will make the right noises to the French to ensure his succession.
Remember, during the 16th century, the French are fanatical about Salic Law. That's the only reason Henry of Navarre became king.
The Netherlands won't revolt. They would see it as them conquering France. It would be the same way when James VI became king of England. The Scots see it as a victory of them over England! The Dutch would only see the benefits of getting to the French market, etc. The Dutch did not rebel when Charles V became King of Spain, so it won't rebel until the Duke of Burgundy become King of France, not unless the King of France does something incredibly stupid to piss the Dutch off.
The French speaking parts of the Southern Netherlands would be indistinguishable from the rest of France. And if there are Protestants, they could easily become indistinguishable politically from the Huguenots.
Even if the Dutch revolt, the French would still keep the southern Netherlands. If Spain did it, the French, much closer, speaking the same language, etc, would keep modern Belgium.
As for the War of French succession, as long as he is Catholic, if the French are willing to have the Duke of Burgundy to be king, and the Burgundians, Dutch, Flemings, etc. are willing to have their Duke be King of France (which in their eyes would be a victory for themselves), what, exactly could the other powers do? I doubt they'd do much. After all, in OTL, they didn't go to war to stop Charles V from becoming King of Spain when he already controlled the Low Countries, and when he was elected HRE, they didn't go to war.
My guess is that unless the future Kings of France does something incredibly stupid, the whole Burgundian inheritance would remain French.