Is there a way, when compiling the text, to remove the inline footnotes without removing the footnotes in the inspector? As far as I can see the choice is between including them both or removing them both; but I hope I’m wrong.
This is an all on/all off toggle as you note. The only thing I can think of that would do what you want is selecting all of the inspector footnotes and converting them to comments (you can Cmd-A to select all, then right-click and select the convert to comments option to do this in bulk). Then they can be independently excluded. To exclude inline footnotes, you’d disable footnotes at the top, then switch comments to export to RTF as footnotes. To go the other way around, just re-enable footnotes at the top, and switch the toggle to strip out inspector comments.
Unfortunately, this trick won’t work if you also use inspector comments for comments already.