On the NJICS, no one has exclusive access to any site. So if you tune into Site 29, you'll receive Rutgers New Brunswick, MedCentral, NBFD, JFK, and all other units in that area that utilize the NJICS on whatever TG their radio is tuned to. If a MONOC unit transports to RWJ New Brunswick, chances are it will transmit and receive off of Site 29 while it is there.
Likewise, you have 5 IRs in Monmouth County alone (which to me seems grossly inefficient and should probably be a simulcast; but I digress) plus the Bordentown simulcast. So, I would bet that you would likely receive TGID 4733 off all 6 of those sites at almost any given point, the most reliable one being the Bordentown simulcast due to its expansive coverage.
Again, it's based more on the proximity of the service than anything else. If a radio cannot strongly affiliate with a site, it will attempt to move on to another. A "primary site" is basically just the site that is most likely for a unit to affiliate to merely because of their service location; a consequence of proximity. So you hear Troop B on West Orange all the time because, well, the radios see it as Site 1 and its coverage is so expansive that it doesn't bother looking for another. All the radio has is a list of control channels and will scan until it finds one strong enough to affiliate with, then attempt to affiliate if that site is in its programmed list. If it works, it sticks; if it doesn't, it moves on.
Also keep in mind that a scanner is just not well-tuned and sophisticated enough to decode any and all signals. What an APX can receive is going to be markedly better than what a scanner can.