So fader does adjust the sound from the two RCA outputs (front to rear etc) even though I'm only using the front set?
Adjusting Fade/Balance on a head unit only tells the head unit to deliver sound and what level to each speaker. If left at 0 or the "middle," all speakers receive the same equal power distribution from the head unit. It's sort of like muting speakers with the head-unit.
And then the amplifier is just a continuous power house for whichever speakers are wired to it. Power is applied via power wires, (-) & (+), and then the RCA's transfer the actual "sound" amongst amp and head unit.
The head unit by using face/balance has no impact on power delivery from the amplifier, you can measure that with a multi-meter. It is all dependent on the internal sound control in the head unit.
So to conclude, yes, you can wire your rear speakers to the factory power wiring behind the head unit, and then wire your front speakers to your amplifier.
Yes it will still work. Why not bridge the two fronts on one channel and the rears on the other?
The problem with running two speakers on an amp and two on the head unit is two speakers will be louder than the others. The only way to get around that will destroy the purpose and sound quality of an amplifier and upgraded speakers.
Depending on how he wants his stereo system setup, he might not have many backseat passengers, thus wanting more sound up front. I can agree with his decision on this one, as I would do the same given I was in his situation. 200 watts isn't very much given it's distributed among 4 speakers.
Another thing he could do would be to turn up the gain on his amp and leave the other 2 speakers alone, so that as he cranks up the stereo, he isn't distorting the sound on the rear speakers that are wired to the head unit. That and if he uses the amp for the 2 speakers, they have 200W to share with each other, and the rear can get their own power from the truck internally. That would produce better sound that splitting a 200 watt amp around 4 times. Or at least that is my perspective on it.
Think of it like this SV, his Pioneer already puts out 50W x 4 speakers, so that means it has the potential to deliver 200 watts. His amplifier is 200 watts. So he may as well use his headunit for power than wiring all 4 speakers to his amp. By splitting amp and internal head unit power, he could have 100w x 2 on each side, yielding 400 watts total. Quality will obviously not be as good in the rear, but it will make due.