Because you cannot have just 1 engineer keeping everything save from it. You need at least 2, if not 3 on certain ships, to keep everything fireproof and still shoot at the enemy. The Gatling as well as the Carronade could be dealt with, with 1 engineer respectively and at times even with help of the pilot. The gunner in the meantime has all the time to shoot at whatever is in sight.
The flamer, as stated before, requires much more effort to be dealt with. But then again, who says the effort isn't worth it?
Think of what the enemy has to sacrifice: A gun slot for a gun that you can counter, a gun that you can render useless. Another aspect in which the flamerthrower is unique: The crew actually can fight against this gun. Every ship that has a flamethrower either has to be ready to fully rely on it's other guns or has to catch its opponent off guard to be useful for the team.
This is, of course, purely competitive, if you get caught off guard and thus get set on fire, something went wrong. Otherwise you are prepared to block the gun entirely. High risk for high reward. Either it works or it doesn't.
Concerning normal matches, and I am saying this again just to make sure, we have to rely on the tutorials teaching new players what to do in case of fire.
Does this end the discussion? Please let us be more professional and refrain from moving in circles or does somebody have something to say that hasn't been stated before?