So I have the dilemma of running games across multiple systems, but I'd still like to know when I hit that sweet cap of 50 NES speedruns. Is it entirely out of question to not just load in all games in your profile as standalone runs, but rather sorted by system category upon you just click each system individually to expand and show said runs and/or an indication by number for how many runs you have for each system.

If I understand you correctly, you ask for a way to sort or filter games in your user profile? SRC doesn't have those options right now.

You can post stuff like that or ideas about what you wish to see in the site, in the feedback thread forum: https://www.speedrun.com/the_site/thread/g79jt

A few days ago, someone else asked for a way to rearrange games in your profile games list as well.