The warnings may go away when you change the property (use main placeholder for popups) to no, but that doesn't solve your issue. Doing this will mean the whole layout is loaded in popups, including navigation, header, footer areas etc. I assume this is not what you want.
The solution is to create a copy of your page where needed using the popup layout, and use this page instead of the other one when you open it as a popup.
Yes, this is a pain - there are probably a lot of forms, and for each one you need to determine whether it is opened In Content, as a popup, or both. If both, you need to create a copy of the page with the alternative layout, then update your usage accordingly. For a large project this can be a long and tedious process
There is a new search anhancement in version 5.13.0 that enables you to search for instances where forms are opened as pop-ups which will help find where you need to make changes
What happens if you open the layout and set the property use main placeholder for popups to no?
Thanks Arjan, all major appstore content is now correct except for: MxModelReflection.ValueType_View (Should be Popup)