Just found the Flatten epub option under EPUB output settings in the conversion dialog. According to the tooltips:
This option is needed only if you intend to use the EPUB with FBReaderJ. It will flatten the file system inside the EPUB, putting all files into the top level.
As for LO Writer, I know from many posts here in MR it can be very useful for fixing conversion issues, but in this case I needed steps that could be replicated easily on a batch of files - so the Xpath Wizard method seems to be OK, as long as the classes are the same in each docx...
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