Yes! All messages sent to the IRC server are counted in the rate-limit, including:
.ban, .timeout, .unban, .mod, .unmod, etc…
But remember this:
If you send more than 20 commands or messages to the server within 30 seconds, you will be locked out for 30 minutes.
If you send commands/messages only to channels in which you have Moderator or Operator status, the limit is 100 messages per 30 seconds.