You are over complicating this thing. You are putting it in personal history, and not hiding it from them. Plenty of people have done and this and got PRs without any issues. Please search this forum and see. There is no functionality in express entry to smartly figure out the country and generate check list like you say.
I'm not sure if you have seen your invitation letter. In that, they will mention the things for which points were awarded. Officer will only cross check that for eligibility. They will see your spouse's personal history to understand what he was doing in those years.