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Looking at it in detail, it's not as simple as just skipping the merge step because of the code that checks for and gathers the EPUBs.
I'm not very inclined to go to the effort of making, testing and supporting a feature to disable the plugin's core functionality for no better reason than "one person asked for it without explaining why".
What about adding empty EPUBs to your book records?
Calibre can do that under Add books > Add empty file to selected books records > Add empty EPUB
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