I see Metal Mario as a separate character nowadays, as the power-up itself isn't even used too often past Super Mario 64. I also think he's cool despite the haters say, but it might be just my overall bias for the Mario character. I liked his introduction in Mario Kart 7 because he's finally a heavyweight I'm looking forward to using (I had some reservations he wouldn't change weight class but that worry was way overblown); we have a Mario in all weight classes since.
He does sometimes read as Mario's rival but I think he's generally chill guy despite what the appearances suggest. You're not alone though, many people do see him as a bad clone of Mario from Mario Generations mod casting him as a bad guy akin to Shadow Mario (or just that he's a perfect fit over Metal Sonic) and you do fight him in the Smash Bros. games. I have my personal headcanons regarding this character too. One big reason I think he's separate from Mario is that he makes phrases that are altered from Mario with no further context; Cat Peach goes like "CAT-astrophe" or something like that, but Metal Mario goes "Mia mama" like he's supposed to be a doppleganger. It would be strange if we had Tanooki Mario going like "Me! It's-a!"
Oh and also why would Metal Mario appear in the same scoreboard as Mario in a Mario Golf game? Is that just an elaborate mulligan scheme from Mario?
Well because they introduced the Metal Box effect and probably didn't have the need to introduce an entirely new sprite when they could just darken Mario's existing sprite. Regardless, I was happy the Metal Mario as a boss character returned in Smash Ultimate as both Bowser's final fight and as a spirit battle.