Indeed you can rotate ("clock") the alternator rear case half to move the stud out or the way. I would also suggest though, that the Ford 3G is a newer and better design, with substantially better performance at the same amp rating. Yes, you can get them under $100, the rear case of those is also clockable, and they fit like Ford made it. LOL You can also keep your gauge functional or your charge (ALT, BAT or GEN) light with them if you have one of those.
An application example would be a Ford 3G to fit a 1994 Mustang 5.0L. Some of the references you find use a Taurus version, which I do not recommend, as they have wider mount spacing and often have clearance or bracket issues.