It’s addressed in detail here: https://github.com/mavlink/qgroundcontrol/issues/6760
In summary: just an artifact of independent development cycles.
The ArduPilot build system uses .px4 file extensions for Nuttx builds, and .apj for ChibiOS (although they are both compatible json files for the bootloader). FMUv5 is only built with ChibiOS, so QGC wasn’t recognising them.
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