Agreed, it doesn't look like the devs thought this through. Hopefully they'll read this thread and make the change in an update in the near future.
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Rhapsody in Umber ONLY affects the Level 70 uncap fights (Maat and similar).
Those are the ONLY battles affected by this Rhapsody.
It says so in-game when you go to fight Maat, it says something like "Because of your Rhapsody in Umber, you may call trusts in this battle." .....it does not say this with any other mission fight I've seen yet.
MOST Mission fights allow you to use Trusts even without said Rhapsody. It's just, for whatever reason, they missed the 2-3 fight. But then it doesn't matter, because you don't need Trusts for that anyways.
Awesome! I just haven't progressed that far in my story missions, so I wasn't sure if that was going to continually be a problem, or if it was just a couple of rare instances like 2-3 and "The Holy Crest."
I can personally vouch for the ability to use Trusts in the 5-1, 5-2, and Windurst Rank7-10 mission fights. None of them mentioned the Rhapsody in Umber like the Maat fight does.
That said, you really should get Rhapsody in Umber ASAP (Lv55-60). The battle against that thing in Qufim (it looks like a chimera) can be solo'd with trusts at about that level with mild difficulty. Or just ask one of the many passing players on their way to Escha - Zi'tah to help you kill it. It's weaksauce to a Lv99 player.
Not only do you get more of those sweet Rhapsody bonuses, but you are also able to enter Escha - Zi'tah and you get another Trust out of it (Lion II).