Don’t apologise, this is all about understanding things that don’t make sense. In truth, moving data between apps involves many extra ‘moving parts’ we don’t see. So, don’t blame yourself when experiments go awry.
FWIW, I think the bottom of the format stack with reference data—at least involving Bookends—is the RIS format. Referencing is fundamentally broken, with years of digital kludges trying to mimic (human-curated) per-publication formats that also pre-date the digital age (so don’t grok things like ebooks).