Coming in from left field, a much simpler solution would be to have a single instance with 2 categories - one for each of the parent sites. This would sidestep all of those issues mentioned above.
There is plenty of scope to style categories and topics that are within that category via simple CSS using the category-category_slug class.
If you want to make one or the other the ‘default’ or home for a set of users, then Custom Homepage for Groups would be the tool you need.