In Can we remove the 5 second rate limiting on comment flags?, a status-declined tag was thrown on a request to remove the 5-second rate limit entirely. The reason provided was that abuse becomes more difficult to handle when no rate limit exists.
I think there's a pretty simple solution to this question: if and only if you're flagging multiple comments on the same post, do not rate-limit the flagger. This means someone who wants to go through and flag 5/20 comments in one conversation on a post doesn't have to wait 30 seconds to do it. But the next time someone tries to flag comments on a different post, the 5-second rate limit applies.
The most common use case for comment flags that I've seen flags multiple comments on the same post. I struggle to see why someone who wants to flag a specific comment thread should be rate-limited, and I really don't see the abuse case here. With both a limit on the number of comments one can flag at once, and the number of flags one can raise, it becomes the same case as being rate-limited while deleting comments.
This would also enable people to flag multiple comments in a thread more easily, particularly when it's not necessary to flag the whole post, which is also a plus.