AFAIK, Verdun is also not a Burgundian core, so it's possible they recognized they needed to siege Verdun, then Barrois, then Auxerrois or Franche-Comte to get any Burgundian core turf at all. Instead, the rebel AI chose the fastest way to the highest development Burgundian Province they could get to, which looks to me like sieging Charolais, which is protected by the fort in Lyonnais.
Just spitballing ofc, but it seems like a side effect of them spawning in a province without Burgundian culture, and the only way from there being through a fort with neighter a core nor culture desirable to Separatists.