It runs the program. I don’t know what’s confusing. It isn’t a translation of anything because “run” in the computer terminology sense doesn’t get translated for the Japanese. It’s just run, or rather RUN, maybe.
If you’re asking why NEC didn’t copy every single name feature and button from the Famicom pad I’d guess either they had their own take or maybe they just didn’t want to look lame to a very important partner. The “start button” only existed on one other controller before, right? Sega didn’t have one until MD, Sony was making stereos back then, MS was just really getting into Windows, no Neo yet, etc.