Literally everything I wrote was in reference to that finale, NOT his first appearance. So yes, being the source of strength his cousin needed him to be, his lack of ego in being so proud of her that she beat him, providing the information about the Dakkam-Ur to use against Rhea, giving her guidance and teaching her moves before the fight, and providing words of encouragement when she was at her lowest emotional point in their last scene...that was all Superman. Not to mention the side characters were still fawning over him as they always do. And he wiped the floor with any Daxamites who faced him and casually took out 3 of their warships in 3-seconds like it was nothing. If you want to overlook all that because they had Supergirl beat him in a fight (on HER show) and had him acknowledge it with pride, well, that's your prerogative.
As for giving her villains to him, well, it makes more sense to me than giving Batman's storylines to Green Arrow. At least Supergirl's in Superman's family and shares those villains with him in the comics, and we aren't gonna be seeing Supes deal with most of those characters in a Superman show or movie anytime soon, so why not utilize them. And we know Supes in that show has had previous adventures with Batman, fought General Zod and Lex Luthor on multiple occasions, fought Mongul on Warworld, Reactron, Lobo, and likely countless others to have earned the reputation he has on that show. Just because Kara's gotten some of his smaller-scale villains first doesn't mean he's just been sitting around.
And Supergirl had a co-headlining title with the Legion in recent years in comics, so tying their origins more to her (especially with her romantic connection to Mon-El in the show), made a certain kind of sense in this case, imo. And they explained the lack of Superman as inspiration because Earth's history was lost to them. So it's not like they just found Supergirl more inspiring or something. Mon-El founded them and Kara was HIS inspiration because he loved her. Again, it's not like there's a Superman show out there that this is stealing from. This is a Supergirl-centric show, so it's only natural that elements of the established Super-verse have become more Supergirl-centric within it. Superman is still held in VERY high regard on the show, so they obviously respect him. Just look at the story Jimmy Olsen told about he first time he encountered Superman, and what he meant to him.