Tom and Marco didn't not stand each other because they never really spent time together. Tom just disliked Marco by default because he was a boy spending time with Star, and Marco thought he was dangerous and a creep.
However as soon as they spent time together that wasn't about Tom trying to get Marco out of the way, the immediately found out they have chemistry and get along well.
However, Marco had been around Janna since kindergarten and still loathes her. It's different. The reasons for disliking her aren't "she's a rival for Star's hand", they're "she's an annoying and awful person".
Tom and Marco are quite alike. They both occasionally get frustrated by Star's antics and yet admire her for being so free - yet it grinds Tom the wrong way much harder, he was still salty about Star breaking the rules in ping pong months after they broke up. Marco is way more tolerant of crazy smugness and teasing - so if even he can't stand Janna it's extremely unlikely Tom can.
Unless the writers go full hack and rewrite their personalities, but I hope they won't. Maybe they'll keep Janna kinda ambiguous for that precious queer representation - Star, Jackie, Ponyhead, Kelly, they're all dating and very into boys, so if Janna will be shoved into a het romance too it might be a bit much