You said: "I have contacted Support re my observation that since v. 3, other spouses are searched for in a relationship search whether the check box is ticked or not."
I just checked an ancestor search with and without the check box. It worked correctly for me - using my son as the starting individual my second wife was either present or not in the result list depending on the checkbox.
What specific search criteria did you use? Perhaps that would help clarify matters.
Be sure you have the "replace list with those found" selected....