I don't think that just because Charles is married to Margarethe we're gonna see the Habsburgs and the Valois teaming up to do anything anytime soon. If Anne isn't in the picture it works better, since if she is, she's either married to an English prince or to Maximilian (I'm never sure why he didn't offer her to marry Philipp - the Burgundian estates would give a lot more to him than his old man?). And if she's married to a Habsburg, they have a nice backdoor into France they can exploit to bring pressure to bear on the French king (I'm not saying they would, or even that they would be successful if they did, but I think it's a realistic assumption that it's going to be a thing in many people's minds).
So, I could see if the Habsburgs were by some circumstance (although this would probably be close to ASB since the POD is in the 1480s and this only happened from 1497-on.) to still inherit Spain, the French ass is starting to nip at the prospective encirclement. So, I would say France is going to still look for non-Habsburg allies abroad - hence why I suggested a marriage between Charles' eldest daughter and the king of England. (Although, interestingly enough, a good way to solve this problem would just be to avoid Richard of Gloucester's usurpation - Edward V lives, he could marry Anne of Brittany (which means her duchy isn't controlled by Vienna; if she died in infancy the point becomes moot); Katherine of York marries Juan of the Asturias (since Margarethe is marrying Charles); Charles-Margarethe's eldest daughter marries the PoW.) So, I could see a Valois-Jagiellon alliance still being on the cards.
As to Anne de Foix, it's given me an idea:
Anne marries François, Comte de Longueville.
Vladislaus marries Germaine de Foix
Longueville's OTL wife, Françoise d'Alençon marries into Italy - like her sister. Maybe to one of Ludovico/Gian Galeazzo Sforza's sons (after all, Charles is worried about Naples, it was Louis XII who had the claim to Milan)