Missiles and civil aircraft engines both spend most of their time at steady-state cruise power, in straight & level flight.

Mil tactical engines get cycled a lot, and are subject to a lot of maneuvering forces. Even more so for a trainer.

You could argue the engine wasn't "designed", or optimized for that role... but how much would a clean-sheet engine cost? Those costs have to be balanced with the utility. Sometimes cheaper in the long run to use off the shelf, even if that's not the perfect technical solution. I'm pretty sure the B-21 engines are something off the shelf, they simply buried it enough ducting to provide the needed LO and airflow characteristics.