Thats odd because I once created a party with two multiclassed gnomes, a mage and an illusionist. I assumed that IWD2 would be no different from Neverwinter Nights in this regard (i.e. specialists = wizards).
However, the gnome mage/rogue suffered from a penalty.
Only way to be sure would probably be to create a new party with a specialist and give the char (via console or dalekeeper?) enough experience points to level up and multiclass.
It should be noteedn the char screen (unter "favored class") if the char recieves a penalty or not.