Are you trying to do too much?
As of now this will strip 'book level' margins from >99% of commercially published epubs. And those are the most annoying ones.
It will potentially screw up the formatting of Calibre generated epubs, and a variety of bespoke epubs.
Calibre generated epubs should be pretty good candidates for epub-epub conversion by Calibre.
Some bespoke epubs really need to be be adjusted by hand, or not at all.
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