>>11895408
Yeah, it sounds like you'd go to the same locations, but are following UNATCO orders, and have to kill the people you allied with in the other route.
The only major question is ending? I think you would still have to kill or face off against that dork in Area 51. Might be a late game betrayal, where JC finds out he's behind it all, and he tries to kill JC for knowing too much and no longer being useful, so you get the same kind of endings.