Yes, I see your point. Rear projection would be good for everyday use. I have a projector in my basement that will be used soley for HT, with console gaming and sport's night the odd time (don't wanna burn out the bulb too fast- they're expensive
).
Good idea to pre-wire both rooms; it certainly doesn't hurt. Better if you can go in yourself and do it- that way you won't have any doubts. In most cases, the builder just gets the electrician to run the wires- and they may think they know what they're doing, but I've seen an electrician's handywork when they ran and terminated CAT5 cables- plain stupid!
In my house, they ran RG6 straight to the basement and then just cut it so that about 6 feet was dangling. They didn't even bother to run it right to the breaker box where the cable feed comes in. Again, STUPID!
Even with speaker wire, they may be just run electrical wire along side the speaker wire for convenience. When you talk to your builder, make sure you are very specific about placement and how it should be run, otherwise they'll just do whatever common sense (or lack thereof) dictates.