If both files would be really identical, why would you merge them? So I think to understand your question I would need some more information.

If you want to be able to place the footnotes wherever you want you could use endnotes instead.

In the layer panel you have a list of all objects. So can easily find empty text frames.

You mean the line which shows that the text frame is chained to another frame? Is there another frame behind your first text frame? Or is this chained frame placed in the first text frame (I don’t know if this would even be possible)?

I used to work with Calamus before switching to InDesign two years ago. And one of the things I was missing since that was the flexibility with footnotes: In Calamus you have to create separate text frames for the footnotes and you can place them everywhere on every page of your document. So it is only a matter of where you place the footnote frame (or the footnote frames) if you call them footnotes or endnotes. And you can place two footnote frames side by side to have the footnotes in two columns. Or you can place the footnote frames on top or in the middle of the page. If you have very long footnotes that don’t fit on the page you can decide how much lines you want to keep and how much lines will go to the threaded footnote frame on the next page simply by making the frame a little higher or smaller.

On the negative side you have to care yourself if the footnotes are all on the corresponding page. That can be a lot of extra work if you have a scientific text with hundreds of pages and footnotes.

Well, and now InDesign gives me a part of the best of both worlds with footnotes and endnotes.