We are looking to add this. In your timeouts, you can include a tag @target-msg-id, which will (eventually) remove the specific message targeted.
ex: @target-msg-id=1234-1234-asd-asd PRIVMSG #xangold :/timeout xantest 600
This has no impact currently in our website, but the backend supports it while we get the necessary things in place for the frontend changes. When it does, we will document this more thoroughly on our IRC.md page.