I have the same issue. Here is one possible "answer":
Before F2P, certain Retrofit ships were available for promotional tokens, the TER among them. This was before the cloak was a separate console.
Now, those "earned" ships are essentially character unlocks, the same as any rank-up ship. They cannot be reclaimed on any character. They do not count towards purchasing a Fleet version.
If anyone can disprove the above beyond a reasonable doubt, I would love to hear it.
I certainly believed I had purchased the Defiant in 2011, but it's possible that I'm remembering the MVAE instead, which the C-Store does report properly as purchased.
The lack of a paper trail is certainly a concern, and not for the business.
I agree with you 100% Thats how it was explained to me by a GM (only after a "few" support tickets lol )