ElDiablos, be aware that unless you have an open-back cabinet that you will also have to accound for the length of RCA connections, HDMI, etc when the AVR is pushed all the way back into the cabinet once everything is connected. This added about 1" to 2" to the depth for me, since I'm using some heavier cables with locking RCA connections, and some heavier speaker cables with banana plugs that stick straight back (no L-connectors.)
I ran into a similar issue when I looked at buying the 5008 and tried to find an under-TV shelving unit to hold my componts. Nobody makes shelves as deep as this monster. I'd even built my own AV rack to hold very large gear some years back, and this barely fit my AV rack as well.
As for the amplifier on the AVR driving 2-channels versus 5+ channels, just keep in mind that the amplifier section, wile very good for an AVR, is still using a common power supply (as opposed to individual completely isolated monoblocks) so whether driving 2 or 9 channels, that one Toroidal Xfmr is supplying the juice for the channels in use. As such, the less strain you put on that power supply, the more headroom it's going to have, the less heat it's going to generate, and so forth. That's the simple answer to it's ability to drive your rears using an external amp for the front 3 channels.
Personally, I'm using Adcom GFA-5x5II series amplifiers to handle everything for my living room with the 5008, and just using the Onkyo's own amplification section for zone 2. I'll admit though, that I'm using low impedance loudspeakers, and the external amplifiers are just a better solution for this setup than any AVR would be. That isn't the case for everybody.