You don't want to be copying stuff to Sigil's scratch (temp) directory. Bad things can happen. But then the plugin's code doesn't indicate it would be looking for the custom style.css file in that location in the first place.
Did you make sure to run Sigil's Tools > Restructure Epub to Sigil Norm before running the PrincePDF plugin? It sounds to me that there are some pathing issues you're running into.
As per the plugin's notes from the first page:
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This plugin does not support non-standard epubs. Select Tools > Restructure Epub to Sigil Norm before running this plugin with Sigil 1.0 and higher.
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