"OK -- so it was popular among people who actually lived in his jurisdiction and unpopular among people who lived outside it (and therefore had no say in his prospects for re-election)."
Are you implying that if Rudy had run for Senate (which he was prepared to do before prostate cancer took him out), his stand on Cuomo would not have hurt him with Upstate repubs? Wouldn't he need those votes in order to win that Senate seat? Since that decision (to endorse Cuomo) is being dragged out now (10+ years after the fact), I'm pretty certain it would have been dragged out during any Rudy Senate race at the time.
In retrospect, I wonder if his 1994 endorsement of Cuomo and his bizarre brand of "conservative" politics in NYC was part of a plan to run for governor of New York down the road -- as a DEMOCRAT.