And still an issue 
I use vuhdo and one minute the empowered spells will work, next time i log in they won’t super annoying bug.
Still not working properly with mouseover macro. I just talented Font of Magic to make it work for now.
I solved it with Vuhdo, since you can link a macro name instead of a spell. You have to press the square again to select the empowered level though. This is the macro I used:
#showtooltip
/cast [@target=Vuhdo][] Spiritbloom
The macro only works if you hit the macro button again on whatever spell level you want to cast at if anyone was wondering.
still present as of today
I just want to add the problem is still there. Every time you unlearn “Spiritbloom” the macro starts to state you don’t know “Spiritbloom” despite being talented into it. The only fix I’ve found is to completely re-log in. The second you “forget” “Spiritbloom” again it stops working.
I got it to work, by doing this:
I made a macro:
#showtooltip
/cast [@mouseover,help][] Spiritbloom
I called it Spirit macro.
In Vuhdo (my frames / click-casting) I assigned my mouse button to use/cast Spirit macro.
This worked. It started charging on first click, and casted on second click.
I sure hope this helps somebody! 
Still there. Switching specs caused spirit bloom not to cast with Clique/macro. Left clicking the spell was the only way to make it start casting. Logging out fixed the issue.
This shouldn’t need Clique or Vuhdo to work. The whole points of adding click casting was to make it so these add-ons are no longer necessary for healing, and that is true for every other class. But you cannot use Spiritbloom in this way. I don’t see any reason why clicking a second time on the raid frame or portrait of the person you are targeting for the heal shouldn’t stop your empower in the correct tier. So, bumping this. Empowered abilities do not work with this new feature, which was a major addition to the game for Dragonflight.
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Thank you for this. <3
Also, the bug is still present today.
The bug exists in Clique and Vuhdo too.
Just want to say this now works with Blizzard’s in-house click-casting, so while it isn’t ideal, it is a legit workaround.