I can't say I've noticed you being too military. I suppose it's possible to be too *human military*, and not take into account for alien differences, but I don't recall you doing that either. I am minded of a fic wherein there was a human-style ban on officer/subordinate intimacy, which led to a rather silly result in the idea of Optimus Prime being hard-hearted enough to kicked two Autobots out of the army for being in love.

Kup has hella clobber. Somewhere in the late issues he threatened to relieve Optimus Prime of command, and Prime took that very seriously. Not sure why him specifically.

Yes, you're right about Ark Duty, forgot that one.

Possibly a lack of exposure to the concepts?