We usually handle this for large scale experiments by manually uploading a separate database table with all our Per_Image metadata columns (compound/hairpin/control, dose, etc). Then the simplest method is to JOIN the tables by adding the metadata columns onto the Per_Image table. CPA then has access to these columns fro GROUP or FILTER operations.
This is the procedure we use for MySQL databases, at least, and though I have limited experience with sqlite, I assume the same procedure would be useful.
The other, equivalent method would be to use LoadData instead of LoadImages, and add metadata columns directly into the CSV that is used.
But, to your question, yes, I don’t see why you couldn’t add (manually, or via custom scripts) to your Setup.SQL database queries to JOIN pre-configured metadata tables that contain your Control wells.
Does that help?