The helicoils are longer. The threads are deeper. I use a stud with more base thread to root it deeper. That is the one benefit to the pad being taller......more engagement. I just put the rocker stands in the mill and cut them down. It's not a big deal.....just not a bolt-on and go.
Biggest problem with milling the pads is that you will have to pull the helicoils out so you don't destroy an end mill, and then you have to put a shorter one back in there, defeating the purpose of having more thread engagement. If you cut the stands down, the thread hole is still on the same plane. There is effectively no difference in shaft placement in doing that, or milling stands.....the shaft would end up in the same spot.
The valve cover rail is not raised.
If you want to use their cylinder head, milling the stands is really not a huge deal. It is just a couple of hours of checking and milling. The checking always should happen on any head, and sometimes a change of some sort is required on any other head, depending on valve length, rocker arm, or cam lift. It's just part of building an "other than stock" engine. Just my opinion.
Brent mentioned that I had made suggestions to them about their manifold. I talked to them at the Cobra Jet Reunion. I had just finished a Trick Flow manifold before I went there. It had no drainback provision to get the oil out of the cylinder head oil drains. The man I spoke with said they would address that. I have done four of those intakes, and had to mill the drain into all four. Maybe they have fixed it......not sure how many were in circulation at the time we spoke. I don't think gasket thickness is enough space to drain the oil back. If you buy one, be sure to check for that. I mill the relief in there, but you can fix it with a template and a die grinder.....just FYI.