Yeah, I think they try to make each rank seem more "immersive" by making a a "special" mission, where you have to go back to your home base and talk to "Da boss man" ... Just for him to say ... "err yeah, well done and um good job, now go and kill some more things"
Then you get the token. If you miss out on that quest, or accidentally skip/decline/cancel it, the Token isn't automatically awarded.
It should be awarded automatically at each rank, but then players would just skip/decline/cancel the mission and that would make Cryptic sad ...
The problem is, "Test Of Mettle" is granted AFTER you get the ship token (it is a mission to "test" your new ship). So, i dont think doing that mission again will give him the token. But i dont have any idea so.. trying doesnt hurt.