If not, you can mount your amp and farad cap in there. Search my post history in general and you'll find my post with pics of how I did mine. I have an Alpine digital amp which generates practically no heat what so ever. I've never had it cut out either when turned up.
Below the "rear deck"... the thing behind and between the seats is the fuel pump assembly. about a foot apart in the middle of it is where the wiring leads go down into the fuel tank. You're gaining MAYBE 1" if you cut through it and IMO, it's not worth destroying the rear deck for that. Your better bet is to mount the amp on top and build an amp cover.