Hi Ddeveaux, I think I understand what you’re describing in general terms. Would you be able to write out some simple steps to follow for reproducing this?

Two Custom Metadata Objects:
Obj1_mdt
Obj2_mdt

Obj1.FieldLookup_mdt is lookup to Obj2_mdt

In Skuid when I select Obj1.Fieldlookup.mdt for my model, Skuid will add TWO fields by default to the model.
FieldLookup_mdt
FieldLookup.Name_mdt (This is what is incorrect. This field is called FieldLookup.MasterLabel_mdt for Custom Metadata.)

I can assume Salesforce just wanted to clearly distinguish these objects from regular objects in backend.

When the name field is automatically added, are you then able to remove it in the builder? If not, I’d recommend looking at the page’s XML and seeing if you can remove the unwanted field definition from there. 

This was just posted as a notification to the programmers at Skuid. The workaround to delete the field is easy enough but this is something I’d think Zach and Co would want to make sure is on the punch list.

That’s much appreciated. I will pass this along.