When going through to add some spell effects to my mod, I realized that something wasn't working right, so I did some exploring. Here's a synopsis:
With a custom Wraith faction, if I design a unit it comes out as Race: Wraith, as expected. If I close the game and start a new game, I can train that unit now (cause it saves it in the mods folder), and it shows up as Race: Wraith again, no surprises there.
The weirdness occurs when I use trainable skeletons. If I design a skeleton unit, it shows up as Race: Undead, as expected. If I restart the game, and start a new game, I can train the custom skeleton unit I created earlier, only now when it shows up it is Race: Men. I looked in the automatically generated XML file for the custom creature and noticed that the <CreatureType>Undead</CreatureType> entry is not inherited. I would assume that it would then defer to racetype of the faction that generated it, but that would have made it a Wraith. I'm not sure why it's showing up as Men...