I've had a quick look and don't see an option that may help here, and I also don't spot an existing request for it either.
I'm happy to log it in our internal bugtracker but could I ask you to send over a "before" and "after" table definition that triggers the behaviour you're wanting to avoid so the development team are understanding you correctly? You can post that here, or mail it in on your ticket (F0068435 in the subject line).
You may also want to add it to our Uservoice
site for SQL Compare so other users can vote-up the change.