I'll take a look and let you know what I find. I've already made changes so its possible that the logic will remove the ships from the market when I load the save. If that is so, I'll disable the setting that does that and see if they show up. If they do, then hopefully that means the issue was fixed.
From the save, I learned that there isn't any vanilla ships in any market (nothing came up that was removed in the log and it checks every submarket in the sector) so I can confirm that its working as intended. The Hammerhead (D) that you saw was, in fact, the TC version - but the TC version has the primary medium weapons changed to ballistic. I went ahead and removed that from being part of the damaged hull in order to avoid future confusion.
Checking the code after confirming that the freighter you get
is a vanilla freighter, however, I confirmed that its hardcoded by hull id. So I will have to remove that mission and replace it with a TC version.
The surplus ships mission uses the faction's known ship list, and so this mission should always give TC ships assuming the default mod settings.
Alright, now on to admins, officers, mercs, and agents...