I can't reproduce the issue. I loaded your project and pressed  calculate 
optimal size. The results was 53352x6474 (with the black border).
Then it tried "Fit" + "Calculate size"+"auto crop" to get rid of the black 
border. The results was "53199x2785". This is in the range, you expected, isn't 
it.
The change of the crop during stitching I can't reproduce. I set the crop and 
this one was used during stitching. Maybe there was an unintentional mouse 
click?

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https://bugs.launchpad.net/bugs/1815854

Title:
  Hugin (et al.) vertically squeezes my long panorama

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