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.
Ok, and? It shoots bursts of flame less often = less opportunity to do DOT as well.
Point stands it's better to debuff a cheap AEC than an expensive Croc. Only debuffing the flamethrower sounds good on paper, but in reality it's its main damage dealer against infantry and you end up with a slow command vehicle that already has a limited aura radius anyway, so you can't get as much value out of it.