Once again the rules are too vague to get a clear ruling on this, imho.
Regarding the original post re control rig bonuses, I've attached my rigging cheat sheet, which just references the RAW. It's not necessarily "right" or "wrong", it's just what I've managed to gather from the rules (and various threads) so far.
Regarding the agility vs logic debate, it's too vague to say (my cheat sheet says agility, but that's subject to change). However, it seems that reaction is used for jumped in piloting of a vehicle, which is a physical stat, so I would guess this is an argument to use agility, but not a particularly strong one.