So although its not ideal, this is intentional - and here is the reason..
In order for WarMode to provide protection it needs to know who the attacker is, and who the victim is. For most entities/projectiles the information for who the attacker was is sent along with the projectile. However, for whatever reason, Facepunch doesn't provide this information for fire, so for any given fire entity there is no saying whether it came from a pvp or pve player, and therefore WarMode cant apply rules to it.
So we could have it just always allow fire damage, but this is an issue because pvp players would use this exploit to raid pve players bases. So alternatively, fire damage is just disabled to prevent these exploits, at least until Facepunch makes the attacker info available for fire.
This only happens when there's a TC because WarMode doesn't provide protection for most things if they are outside a base.
Its also worth noting that its only the fire damage over time that is disabled. The initial fire damage from incendiary rounds/flamethrowers/molotovs and whatnot should still follow rules appropriately.
Hope that clears things up - going to close thing one since its intentional.