The speakers and next is the room and finally the receiver/amp/transport. You can hook up different speakers to the same amp and theyall sound slightly different and then play them all back in a different room and get even more different sounds, but change out those electronics and the differences are much less noticeable.

I have M3's sitting in a bookshelf and they sound great! Bass response is unchanged from when I had them outside the bookshelf. I only have 3 or 4 inches max clearance for the ports.

Biggest issue may be keeping items on the shelves from resonating due to the vibrations from the speakers. If you have a good number of books in your bookshelf, then that will add enough mass to the unit to keep resonances tamed.