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If it makes you feel better, Captain Chakotay had normal pips by the time the Protostar was commissioned. Guess Janeway just didn’t want to grant ranks away from Starfleet proper.
I just always imagined an awkward conversation between Janeway and some new species she had just beamed on board: “so uh, Captain, why do some of your crew have different rank pins?”
“Oh, you mean the terrorists? Don’t worry about it, they’re fine.”