I seem to have found a workaround for this problem. It's not great, but if you use it from the beginning, it seems to work okay.
If you already have the transformer in the system, copy it (ctrl-c). Now, delete it.
Next, paste aligned to same place (or however, you want to get it back in the model). This will keep the name and other instance properties from being deleted.
Next, connect the primary side to the panel that serves the transformer. This should make a new circuit in the exact same place in your panel. If you named your circuit or have conduit sizes or breaker sizes inputted, you will need to re-input these. If everything went according to plan, your new circuit should be neutral-free (because when you attached it to the serving panel, it was a balanced, albeit zero, load).
Now, you should be able to connect the secondary side to the transformer, and the feeder serving the transformer should still be neutral-free, even though it is now unbalanced. You should not have to re-input the information for the secondary side circuit because you did not deleted the secondary side panel.
If you're starting with a new system, if you connect primary first, then secondary, I think this should work for a full project.
I have not tested this extensively, but I have tested it in a model that I am currently developing and ran into the same problem with neutrals on delta circuits.
Hopefully this works for you guys!