Same as Austria not too long before the POD, there wasn't just -one- Duke of Bavaria at this time. The duke in question is Albert IV, Duke of Bayern-München. He wouldn't unify the Bavarias until 1503, before which I argue he is in no position to contest France-Burgundy over Austria. His marriage to Kunigunde was only possible through intrigue, and unless he can muster some marvelous anti-French coalition (which just didn't exist at the time, especially not if the French king inherits the sole rival to his power) within the HRE, it just isn't going to happen in his lifetime (Albert dies OTL in 1508, and his sons co-rule a 'united' Bavaria afterward---they are less likely to push their mother's claim than he is)
Let's not forget that Maximilian I doesn't die until 1519 anyway, negating a lot of these points anyway. Any contest over Austria will have to wait until his death, by which time the succession (by way of the son of Charles and Margaret) will be well-secured.
Not shaky; As the OP says---Philip is dead before Maximilian's OTL death in 1519, by which time Charles and Margaret have a son. The HRE is up for grabs, sure, but Charles' son does inherit Austria by way of her mother. Who contests his claim? In 1519 Bavaria is mired in sibling rivalry, Bohemia-Hungary and Poland Lithuania are busy, and France wins any war over the issue of Austria 'leaving' the HRE anyway, at least initially.
Like I said in my post above, France-Burgundy-Austria is likely united only briefly under the son of Charles and Margaret (if they only have one son, if not then Margaret's Austria-Burgundy likely returns to the HRE, with some splitting of the Lowlands that is more favorable to the French than OTL). Very likely that Austria and some of the Austrian Netherlands + Upper Burgundy returns to the HRE at some point afterward, albeit under a Lowland-born Valois Duke of Burgundy
Perhaps Max might still marry Anne of Brittany or Germaine de Foix and have heirs..