brad bb, I try and run as much plumbing and electrical through standard stud walls and keep it to a minimum in the timbers. I build a chase box on exterior walls for the wire and pipe it also acts as a mounting surface for the electric boxes. For First floor/basement ceiling I am still using timber with drop in 2x stock. My recent job I used curved 32' binding beams and snapped lines for the bottom of the joist, this left the joist almost flush in the middle but at the ends there was a gap of 5" for pipes to pass through with no holes drilled. I feel as I had some reprieve as the electrician took one hour to bore a 2" hole diagonally through one of the end binding beams. He seemed to have some issues with a grk screw. I had mentioned to bore just under the beam, but others seem to have better thoughts.
I don't mind exposed copper I like the contrast and if they do a neat job it it can be attractive. The plumbers are using more PEX tubing today though. You may have to do it your self as the younger plumbers are moving toward more modern material and the sweating may not be as neat. On the other hand red, white and blue pipes could be patriotic. In some older houses where they have put water pipes through post I see a staining of the wood due to condensation but not so much as to rot the wood, a liner sounds like a good idea. On the second floor we are using a joist bay as a plumbing chase, this will be capped off with a wide plank pushed up to the pipes and small pegs inserted for it to rest on. It will be a bit out of place but a lot of other thing in the surroundings are as well, they just all come together for the character. This also works because the joist are not jointed to the tie beam, they rest on top. I think there are a lot of way around these issues we just have to have the plumber, electrician and home owner come on board. There is a trust issue involved and it takes time to develop, I am still working on it. Maybe more grey hair and a higher cost will help, for those are attributes of some of the architects and designers I have seen. This seem to be verging on another topic. Tim