So as an update, it appears my configuration in DSAM was pointing to the wrong directories. I fixed that and all the IDs came over correctly. I was using the vanilla Freelancer install directory instead of the Discovery one.
In other news, I did manage to force my ship to be a Scorpion Gunboat with a Wild ID, but every time I attempt to undock from base, the server crashes. I might have uncovered some kind of race condition, but it’s not clear what it is, precisely.