Yeah Chakra is a bit awkward to use.
In most fights, there's hardly and opportunity to charge 5 stacks, so it's used pretty much only in the opener, with stacks precharged before the pull.

I'm also baffled as to where the Chakra TP skill might be useful outside of large pull trash mobs. If a boss has enough downtime for you to charge it, chances are pretty good that you don't need the TP.