I have scheduled someone outside of my builder and his subcontractors to give our HVAC systems an independent evaluation and to look at the things mentioned in this thread. Thanks everyone for your input, it has been most helpful.
Odds are, a second look a the system when it was close to production probably found a prvious caclulation error that led to the 4 ton unit only producing 45,000 btuh's. The quick easy way to boost that to a respectable 47,000 without a total redesign would be to increase the suction line. It's an easy spec sheet change. They found it worked and now they are closer to nominal. This is likely why the spec for the line set was changed. Bottom line is, if you can cool your house with 45,000, then use the 7/8 if it's an option in the spec.
It's no different than another mfg suggesting the use of a time delay to acheive a higher SEER, they know it wont be done anyway.
I like the idea of switching to a R410A unit that still gets the full capacity with the 7/8ths if that's the case.
My bet still holds that the piston in the indoor coil is too large for that system. I'll also bet that the blower is set up too high even if it is fighting to provide the amount of air it should because of improper return and filtration.