There will be no such logic to find out if a windows is the "main". The concept doesn't exist in the Windows API, and thus trying to add such a concept will likely cause all sorts of problems. 

If a program has such an internal concept, great! But Wine nor the X desktop will know this, since there simply isn't any reliable mechanism to determine this. You could add per-application hacks, but 1. that's not the goal of the Wine project and 2. this would be an extreme amount of work (years) for very little end-user benefit, while also risking breaking applications.