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Well yeah, but the conversion pipeline cant be run (for various technical reasons) inside the GUI, so the GUI basically uses a trick to use an approximation of the conversion pipeline. It works fine in most cases, where you don't have unusual input files, but in some cases, like this, the approximation isn't good enough.
I could of course run the conversion pipeline in a separate process and then take the output of that into the GUI, but that is too much work. I prefer to spend the time just improving the PDF engine so it removes headers and footers automatically.
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