Joan the Mad probably will stay mentally unstable, since that wouldn't be altered, however apart from that external conditions might be better for her ITTL.
Also given the age of Philip and Joan, there most likely will be more children.
Regarding the court of Margaret of Austria in Mechelen (Malines in French), it still was quite Burgundian in style and attracted a lot of artists (including musicians) and scientists (like any court). The education of Charles V and his siblings there was more influenced by humanist scientists than one might think.
Also regardless whether Philip survives or not, Philip and Joan had travelled to Castille leaving their eldest children in the Burgundian Netherlands.
However the relationship between Ferdinand II of Aragon and Philip the Handsome would remain problematic. This scenario might result in OTL Holy Roman Emperor Ferdinand I being named as the heir of the Spanish Kingdoms. Since Philip and Ferdinand II really disliked each other.
If that would happen, then Charles V probably will marry Anna of Bohemia & Hungary instead.