Yes, it tends to happen that bot sends more than 3 whispers in the span of 1 second (not very often, but I’ve seen it happen on one of the bots one of my friends host when streamer’s chat was very active and bot had to reply to many people at once).
I don’t have a very big community myself, but in some bigger ones bots whisper over 50-60 users in the span of 24 hours with plenty different messages, such as: warnings for violating channel rules with timeout/ban explanation to the offender, updates about moderation reports that were made by trusted non-moderators or even replying to moderators, who execute commands such as “nuke” within whispers.
So these rate limits currently present are not sufficient and it makes it impossible to set up and host another instances of these bots in any bigger communities with active communities without risking bot banned from whispers for 24 hours for no apparent reason.