Do not forget that Ingame, the Habsburg are rarely as powerful as in real life. If France was rebelling against Austria, it was especially under Charles V (Quint in French, but i dont know the English name), and the Spanish Habsburg allied with the Austrian one. France was directly surrounded, and this is why Richelieu, then, was willing to support the Smalkalde (Protestant League) during the 30YW which lowered a lot the Habsburg power. Then until the Spanish Succession War, France and Austria were not "rival". France was struggling against UK and Spain, while Austria was controling Ottoman Empire and Poland-Lithuania (and managing an undisciplined HRE).
This was "realpolitik". For instance, the Janissaries knew their first big defeat against the Austrian-French-some german forces during the XVII century.
On the other hand, i agree that an alliance between France and Austria in the beginning is painful. Maybe we could have a modifier like -50relations, (+3yearly) which would prevent an Alliance between the two during the first decades.