Ah, I think I see the problem. The Companion is primarily RPG rules, not rules for the board game. Total Warfare's introduction doesn't mention it superseding the Companion but specifically mentions all of the various board game rule sets (including the BMRr), so are you sure you're not mixing up the rules for the RPG equipment with the board game?
EDIT: Combat Equipment, published after both, specifies the Kobold's micro-grenade launcher as a direct-fire attack. I think that, since ATOW does allow grenade launchers to fire indirectly, this is one of those places the RPG and board game rules diverge.