This post was already answered by Matthew Curland (I'm including his answer as a reply below), I'm posting it again as a reference in case someone else has the same issue.
In the diagrams below, note the two "Id" columns in table División: Id1 and Id2. d2 is a FK to the Empresa table's PK, which in turn it's this subtype's FK for its Entidad supertype's PK.
Also in table Empresa, notice the column DueñaId.
Having the DefaultPopularReferenceModeNames settings shown in the image, I would have expected the hird column's name in table División to be "Empresa", and column Empresa.DueñaId to be named "Dueña".
Do I have any way to prevent these two issues? The Id1, Id2 column names happen in a couple more relational tables througout the rest of the diagram. I won't be able to live with those in the final production database, so I will end up just renaming the column in the relational view, with the accompanying annoyances of having to rename them each time the model is refreshed...