I fitted my changer in the drawer under the drivers seat, with the aid of the expanding builders foam !!!!!, it was a bit of a hassle but it works well for me.
I did much the same thing when fitting my Kenwood changer to my first Laguna 1. I flipped the spare wheel over (there was no spike through the middle like there is on later cars) and then put the CD changer inside, using bin liners full of expanding foam to make a perfect sized insert.
I did worry about ventilation, as these things can run pretty warm. I'd like to say it never gave me any trouble, but the Kenwood changer was a heap of junk from day 1. I should really have taken it back, but after the cheap (well, 300 quid was cheap at the time) Clarion in-dash unit I'd had in my previous car, I just thought that skipping all the time was part and parcel of the in-car CD experience
On the Mazda I had before the Lag, I fitted the changer in the boot but made a metal guard to go around it and offer it some protection. Generally speaking though, I think these things are robust enough to handle most things that are likely to bounce around your boot. I'd happily fit one in the boot without a guard now, though I'd probably temporarily remove the player if I was going to take a load of building rubble to the tip.