I was able to replicate the bug, where if you select “populate content” on an empty popup, it will add the page elements to the popup, instead of only previewing.
But, if you add at least one element to the popup, before you select the “populate content”, it should work.
Let me know if it’s working for you this way. Just a note, it will not change the page behind (there you only see the header and footer), but it will change dynamic tags in your content.
I’ve created an internal bug report about the “populate content” behavior if there are no elements.