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I use GoodReader to do exactly as you describe. It gives a lot of flexibility in how you manage sync records, including being able to store the synced files in different folders from where they’re arranged in the Calibre folder structure. It also happens to be my favorite eReader for reference documents or anything I might want to mark up.
I still use Calibre Companion as my interface for finding the reference I’m looking for, as I like to be able to search by tag, etc. But once I identify the text I want, I just open it in GoodReader via the author-named folder in my library.
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