You'll potentially be missing more traffic. A lot more, in fact.
If you "combine" all three site control channels into a single "site" in your programming, the scanner is simply going to land on the first one it finds active and will remain there. Whichever site's control channel it lands on, that's the site you'll be decoding.
So let's say for example you're in range of the West Orange simulcast (774.78125), the Ramapo site (770.95625), and the Alpine site (769.70625). If you program all three of those control channels into a single "site" in the scanner, as soon as you start scanning, it's going to stop on the very first one it comes upon. Doesn't really matter which one it stops on, because it's going to simply stay there decoding only that site, unless it has a reason to move to another (signal drops out, etc.)
In order to have the scanner check all three sites, they need to be programmed separately so that it will dwell on each site for X amount of time, then move on to the next, then the next, etc. It will cycle around all three sites looking for activity. The default dwell time is probably around 2 seconds per site. Unless of course it finds activity, at which point it'll remain at that site until the activity ceases, then it continues the cycle.
Here's the bottom line when it comes to systems like the NJICS that have multiple sites: you're never going to be able to catch all of the activity by scanning multiple sites with a single scanner/receiver. Especially when some talkgroups are normally only carried on certain sites. You may only get the Passaic County Sheriff on the Ramapo site, but not Alpine. Likewise, you may only get the PIP PD on Ramapo or Alpine, but not West Orange. And so on.
So unless you happen to be lucky and find that one of those sites is carrying most of the talkgroups you're interested in, your only choice is to continue to scan multiple sites and deal with the inevitable missing of traffic as the scanner moves from site to site. If it's checking West Orange and Ramapo while a transmission on the PIP PD talkgroup is happening on Alpine, you're going to miss some/all of that transmission. That's just how it works.
The only solution to drastically reducing missed traffic is to use multiple scanners/receiver...one for each site.