My question is, if alerts are okay and whats the limit.

I saw the fake Todd Rogers run for SM64 and i think this kind of alert is probably not allowed. Who doesn't know the video, here a link with Timestamp (1:50):

Sure i think it depends from game to game, what shouldn't be covered. In Super Meat Boy, the Loading Icon must be visible and i think a run would get rejected, when an alert would cover it by accident.

I don't look for a answer, for specific games. Sure having no alerts over the game, is the best solution but having alerts is for some nice to have.

personally I don't think anything should cover the game like that, if one screen of the ds goes off the camera it can get rejected so I feel the same should be here as soon as the full screen is covered the run should be disallowed :) ofc many other people will have a different opinion. I don't mind little alerts though as it is a nice way to say thank you I guess ^_^ haha this fake run is great though with that super mario sunshine footage and stuff XD but yeah my opinion is its okay if its small :) although I don't stream so idk haha :)

this was only a extreme. I mean the usual alerts, that streamers use. Sure when something fully covers the game, than this isn't okay and i think viewers will also hate this. I talk about 10-15%.

It also depends on the length, if it covers a bit of somewhat important information for like a second I think approving and contacting the runner would be better than rejecting but if it would cover these informations for like a minute, rejecting would be a better idea there imo

If it covers the little girl animation in super meat boy runs, I guess it's a valid reason to reject a run.

Like @blueYOSHI mentioned, if it covers an important piece, it shouldn't be allowed.

This is why I put my alerts over webcam, splits, or empty space. If they have to be over gameplay, it should be as minimal as possible. Runners should consider/plan their layout accordingly.