I think I touched on this very early in the thread (i.e. months ago, but I can't find the reply);since it has been so long I re-tell what I was advised:

During my Global Entry interview I asked about adding my official passport to the system. I was told NO, not because it was Official, but because you could only have ONE PASSPORT in the system at a time (meaning if you have a second 5 year passport, or a no fee, like for Israeli travel vs Mid-east, you could not add that either). I asked about paying the 100$ and reapplying on the second Officia Passport, and was told at the time they didn't know for sure, but he would advise against it, as all of them are linked anyway, and it could cause problems. I will say this was just after the program started, and at a Houston IAH interview (back when Houston was one of the three original airports in the program). However, he did say if I had applied with just my Official Passport initially that would be fine. Maybe this has changed, maybe those on gov't travel don't care enough to do it. YMMV,

I think having the Official Passport helped speed up my interview, along with a fairly high gov't clearance security clearance, but that was never made official to me by an agent. I can tell you I was approved online instantly and my interview lasted less than 10 minutes, including the time the agent took to copy my documents. I also have an Italian passport, and they don't care-the US does not prohibit dual citzenship, but of course you must enter the US on a US passport if you have one.

Good luck.

Ciao,
FH