I have no insight into the workings of bag routings but have done the to/from ISP custom routing thing many times without problems. I surmise that there are so few ISP flights now days that they would take the shortest possible path timewise.

BTW, I just had an incident (published routing) where my ISP-BWI flight was late, I was the last person on BWI-MCI (holding A01), the last night of the flight for the aircraft and crew and passengers and at the gate they told me that we were leaving immediately, on time and wouldn't be waiting for my bag. Did I still want to continue??

Kicker is that we left on time and arrived 20 minutes early.

So they do what they want to do anyway...