What is the best way of managing multisite propagation post setup phase?
It sounds like perhaps the problem you've got is that you're not making fields translatable? That would explain what you said about "Otherwise the content edited overwrites each site page ". The idea is that pages should stay set to propagate to other sections (to the group in your case), and the fields store the translation data.

Assuming that's the case, I think your problem would be solved if you didn't change that to "Only save entries to the site they were created in' and set up the fields themselves to be translatable. That would allow you to create new sites and propagate the pages.