Alien breed at least has the settings file intact, but tower assault doesn't have one and the controls do not match up with the manual, it says weapon swapping is done with alt but alt shoots, as does space which is marked as the key to use the consoles, both control and shift enable retreat mode.

I dunno if that's just the documentation being wrong or if it's specifically the multiplayer controls

It's a bit very confusing since I can't find a key to swap weapons

If you wait for a little while in the Tower Assault main menu, it will show you some keybindings. F5 changes weapons (and F8 for player 2). I would have guessed it on my own :)