I have just found an option to do what I was after - Only group windows of the same application type with each other. I hadn't noticed it before - maybe new with the latest update?
I've been using Groupy for a month or so and in general find it helpful. Currently there are options to 1. Automatically group all windows of the same type together 2. Automatically exclude from auto grouping all windows of a specified type. However, I would find it helpful if there was a further option Only group windows of same type together - e.g. Explorer windows would not be combined with say a Firefox window or MS Word Window