Well, I found a place to customize this, although I still have not found a way to override or extend the linq query for loading the data:
In the file \DynamicData\FieldTemplates\ForeignKey_Edit.ascx.cs (as per default location), in the Page_Load method the following call is made:
PopulateListControl(DropDownList1);
This can be replaced entirely with your own code.
In my case, I first checked if the current table implements a custom interface I defined.
If it does, use that to get the data to bind the dropdown, else pass control on to PopulateListControl.
Using Reflector, it seems that PopulateListControl ultimately uses MetaTable.GetQuery() to get a default list query for a table.
Would have been nice to extent that instead.. but moving on to other things now!