Maybe I'm just a casual and don't know any better, but if this is the main site to submit speedruns across almost just about every single game on the planet, why isn't every Megaman game to exist tracked here? Is this just a community decision?

You're looking at the Mega Man X page. Each individual Mega Man game has its own page.

If a game doesn't have its own page, you can request one be made from the SR.com admin team.

https://megamanleaderboards.net/index.php was around first, and it was already established as the site for Mega Man RTA, so people didn't want to make the change. I'm not familiar with all the nitty gritty of it all, in all honesty, but in subsequent times, there's been behaviour expressed by srcom people that has lead to a negative attitude towards them from the Mega Man folks' side. For instance, asking for permission to add a board for Mega Man 2 on the site, not getting that permission, and proceeding to add the board anyway. Things like that.

The Mega Man RTA Leaderboards site is the main site for all Mega Man games, and the community generally wants it that way - albeit some also wish for the games to have representation here on this site because they want their srcom profiles to show all their times. Hence this MMX board on here.

I'm sure someone could give a more detailed answer about all the lore.