If you lose any pressure, there is a leak, but 1-2psi over that period is likely not much more than what you know is already an issue. I've only used one of these testers over a short period, but once I got the leaks sorted out (loose clamps in a couple of spots) it held the same pressure for over 45 minutes. For all I know the pressure tester itself could be an issue, but I didn't have that problem.
You'd want to check cold, since the checker is "sealing" the system, any decrease or increase in coolant temp from when you start measuring will affect the pressure reading.
While I've seen people run with no pressure in the cooling system for specific reasons, and I've never seen an overheating issue caused by it...the loss of pressure means the coolant will boil at a much lower temperature, which can cause localized boiling (at the cylinders) and that could theoretically cause temp issues. I don't think that is your case, if it will hold pressure, even if it leaks down a bit over time, it's not going to be the issue here. But more pressure is better for this reason.
Sort out the known leaks, then hit it again with the pressure tester. I'd run it over 15PSI (30 was max on the one I had) for testing, if something blows at 20-25PSI, it was a weak component anyway. I would try to reference coolant level before the test, then let the system sit with pressure for 30 minutes+, and note not only what final pressure was, but coolant level as well. If you lose any coolant, it's going somewhere. The longer you let the pressure work, the more likely you are to find where the coolant is going.
Didn't you have the same problem before/after the motor swap? I'd love to blame it on running lean under load because it's not the same cam/exhaust/whatever, but that wouldn't explain the same issue with a previous motor. You have an adjustable AFPR...any reason you can't temporarily crank it up to 14-15PSI and see what happens under a high load situation? It would be interesting to see if that influences your cold idle issue as well.