I wonder if you are just seeing the standard five-minute delay that everyone gets when replying inline in a thread. That delay is indeed intended to discourage too-fast back and forth comments, which sometimes lead to arguments.

If that is what you've encountered, you can bypass the delay by clicking the timestamp of the comment you want to reply to. This opens the comment in its own page with a reply box.

Thanks, but no, I don't think that's what's going on here. What I'm experiencing is 60+ minute rate limits after 5 comments plus maybe 5 edits ("You're posting too fast, please slow down. Thanks."), frequently coinciding with higher karma (15k+) users leaving the first reply and a -1 or -2 downvote balance that usually eventually fights its way back up to +1 or +2. When this happens, I'll try to post every 20 minutes or so to test the boundary. Of course, doing that might be tripping a sliding window, or it might be indeed a stricter rate limit. It's hard to know for sure what's going on. In any case, I don't expect an explanation, if the site is really giving super downvotes to certain users with or without their knowledge, telling people that that's the case would undermine the impact of the approach.

Well, at some point the end-user will have to make a judgement call about the authenticity of the server they're interacting with, but that is no different from what happens now.