The limit applies per connection, not per account (except for JOIN), so as long as you limit each connection according to the rate limits you will be fine. Make sure the bot is modded in each channel to use the higher limit (you should however apply the lower limit to your code, in case it’s unmodded somewhere).
If you find yourself getting close to the limits, you can simply spread out the bot’s actions over multiple connections/instances (let each connection manage a limited amount of channels depending on activity etc)