Nah you wouldnt lose ventilation. The rear seat fram if you look is hollow, a prefect place for a couple Computer fans...can even get them with little neons in them, to pull air out. If you ever get pumped up, take out the back seats and look under the carpet, youll see what Im talking about.
Yeah I had a MTX amp on the back of my seat for a while, worst damn place for it, then I moved it to the trunk, that sucked but in a
stang you dont need a monster stereo like you would in a Caddy or Lincoln.
BTW, when we putting in the 60" MTX in your car, just need to hack off 3/4 of the roof and fenders.