yeah subs are geting compact nowerdays. you can get things like

for not too much nowere days (dont know what that ones like, just used it as a example) and even thinner ones. not sure on the sound quality and personally ide prefer a proper sub.
you could always make a false floor and put the sub in then put a guard over the sub, this is what im going to do. will get some pics up when finished.
but if you oftern have things in the boot something small could slip onto the sub. in which case a arch build sounds good.