My tampermoney recently gave me an update notification, that it would need permission to run user scripts. I checked my config, and it was already activated. You need to click details to show the additional config options, and there will even be the Itch domain listed as the domain this extension is allowed to do things. Maybe this permission is not activated on your browser or the Itch domain is missing ("https://itch.io/*").
I just tried it with Chrome 149.0.7827.54 and Tampermonkey 5.5.0. The tampermonkey icon will show a small (2) as soon as I visit an Itch page and both scripts still work.
the chrome extension can only exclude one tag at a time and it does it by adding the exclude header into the URL. Example: ?exclude=tg.visual-novel
Yes? That's what it is supposed to do. The tampermonkey scripts are happening user side. The exclusion is happening server side. See this thread https://itch.io/t/160014/can-i-use-exclusion-filters , where the exclusion filter was introduced.
All my extension does, is to give the feature a box to just enter visual-novel, instead of writing the whole thing in the url bar. And it makes this modification persistent. If you add or remove another tag, it will vanish otherwise. It will also stay beyond a browser restart.