I’ll try it, thank you!
As far as I can recall (not used Margin Note since I went on my Great PDF Editor Quest), Margin Note imports PDFs into its own custom/proprietary system on opening. Changes to the PDF aren’t made to the original file because the app is not editing the original file, and any changes to a file that you want to see outside the app will need to be exported.
For what it’s worth, Margin Note also handles PDF annotations in a non-standard format, making them incompatible with other software. This is a necessity of what the app does, and for many users this isn’t a problem, but given that you’ve already found a spot of friction for yourself I would nudge you to question whether the app’s benefits mean non-compatibility isn’t an issue for you.
PDF Expert, which you mention, handles PDF annotations and mark-up in a standard format, meaning that amendments to a PDF file can also be interacted with by other software, and does not require its own internal system for handling PDFs. This is true of various other PDF apps as well.
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