It is a different ship with different skills and stats. Unlocking the mastery on a c-store ship was never designed nor intended to affect the fleet equivalent.
Please realize that x-upgrades are separate for fleet and non-fleet versions of ships as well. Sorry that you didn’t realize this.
Run the nith rule patrol on elite one or two times—you will have your mastery filled in no time.
Maxing out the C-Store ship unlocked it's Starship Trait.. so you didn't waste your time.
But as explained above, the fleet version is a whole different ship, and you need to level that one as well. Fleet Ships don't have a Trait so you only have 4 levels to do. The trait you unlocked from the C-Store ship can be used on any ship you fly so you can fly the Fleet Version with the trait you got from the C-Store ship.
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Please realize that x-upgrades are separate for fleet and non-fleet versions of ships as well. Sorry that you didn’t realize this.
Run the nith rule patrol on elite one or two times—you will have your mastery filled in no time.
But as explained above, the fleet version is a whole different ship, and you need to level that one as well. Fleet Ships don't have a Trait so you only have 4 levels to do. The trait you unlocked from the C-Store ship can be used on any ship you fly so you can fly the Fleet Version with the trait you got from the C-Store ship.