interesting problem.
I think reputation is quite good, but blanket enforced limitations should be there only to stop ridiculous levels of commenting, like 20/30 per minute or something. Customization options for the streamer could be sensible though, so if the streamer themselves decided they only want users to have 1 comment per minute, then why not? If their audience doesn't like the level they set, they can let them know.
For the audience, if you've got rep, or tags of some sort then you can use filters perhaps? Like maybe you only want to see comments from people with rep over 70.... or maybe you only want to see comments with the tag 'Question'. If these filters could be adjusted in real time then you could have a much more dynamic and personalised chat experience, and if people abuse the tags you can downvote them. Maybe downvotes are only temporary, so enough downvotes can make you temporarily invisible, but your rep creeps back up to a default minimum on a cooldown. I suppose you could have two rep scores, temporary and overall, so temporary rep could boost a new users question super high, or temporarily reduce a rogue whales influence if they are losing their head in a certain chat or something. These incidents would effect your overall rep slightly, so that only repeated negative behaviour patterns could eventually drag you in the attention gutter.
I dont know if people would appreciate the tags concept or not, but it seems to me the host could customize certain tags for their audience to use....so if you want to encourage a specific topic you can add that as a recognised category.... like 'cats' or something, or maybe its a question/prompt posed by the host like 'share a funny story about your cat'. That way you can easily filter the chat to be only responses to that particular prompt, and if thats being abused you downvote it. Plus there would be a bunch of standard shortcut tags like q for question, m for meme or something, one for positive feedback, one for throwing shade, lol. Imagine how fun it would be to filter the chat to just everyone whos hating on you? Such mental health.