The flamethrower debuff is quite noticable, because cooldown between bursts gets doubled and the main reason you get the tank is scorching infantry not as oversized Cromwell.
I'd still say making the AEC a command vehicle is your best bet, besides some rare situations where AI is not your main priority for the Crocodile, but you mostly want it as meatshield for a pair of Fireflies.
I am not so sure that the flamer damage comes from weapon and not the DOT, in any case it the one of the weapon that get affected by they penalties the least.