Just wanted to know is it or not, would be great idea to a category for speedruns

No, cheesed up rewrites CYOP and a lot of other parts of the base pizza tower game so there's no telling in what way it differs and gives an advantage. Unless there's a level designed for a specific CYOP fork the only versions allowed are base CYOP or the speedrunning hotfix.

What if it requires AFOM to play? I know that's been a new thing recently.

That's what "Unless there's a level designed for a specific CYOP fork" means. If a level is made specifically for AFOB (or any other version of CYOP that adds new objects/mechanics) then the category will be using that instead, otherwise only the base CYOP version or the hotfix are allowed.

Wait so does that mean if you do a run on AFOM of a level/tower that doesn't require/add to it it'll be rejected?

And also would you check any of the teamstre era submissions for signs of AFOM in that case or is that too much hassle

I guess that really depends on if AFOM changes anything drastically. Other than extremely small tweaks and new objects, AFOM is identical to CYOP (well, it fixed things given its name), no existing objects change enough to disqualify it being used in non-AFOM levels. Although you really shouldn't use AFOM if it's not needed.