Did you check criticals or just damage?
Because I believe flamethrowers do a bit of their kills from out of control man criticals.
Their crit tables are identical too.
Keep in mind I'm only looking at the engineer and pioneer flamers when I say identical. The Croc/flammewerfer HT are the same in terms of crit tables but obviously differ in damage, range, etc . Flamethrowers are highly random, thats why sometimes it burns forever but doesn't seem to kill anything.
Commandos are fairly robust against flamers as infantry goes, they have 70 hp/man, 6 men squads and soldier armor(which is ignored by flamers). Its like trying to burn airborne.