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Yes, the tkinter/Mac pop-under issue is well-known. I'll add Kevin's workaround if I get around to it. The next Sigil version will include PyQt5 which won't have the same problem. The plugin is already ready for this eventuality.
As far as the OPF line-breaks go ... I wouldn't know. The output passes EpubCheck (so long as the input did), and I only ever edit epubs with Sigil--which would reinsert line endings whenever I opened it anyway.
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