Gains are used to match the pre amp voltage to the amp, you cant use it as a safety precaution, gains wont do anything if there is a surge. and you will lack performance because they arent set up right and you not getting max performance out of the amp.
But you stilll have the issue of poorer performance because you have to have it lower to protect it. Wouldnt it be much easier to use a 4 awg and buy 0 awg power and ground cable. if you needed it, wouldnt cost that much.
id run 4awg to the boot, if your sub is that pioneer i think i read about? this gives you the option to upgrade (as mentioned) to a bigger "bass amp", or even the opportunity to add a second amp (via a fused distribution block) to run maybe some components up front.