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It actually seems like a sane choice to me. PDF is good for rendering, but horrible for parsing. DOCX is a ZIP file with XML data. Maybe ODT or whatever would've been a better choice, I don't know what the format is like. But if you disregard the usual knee-jerk "but it's Microsoft!" reaction, it doesn't seem like a bad choice.
The Office Open XML file format is extremely complex, and takes up around 6,500 pages (compared to ~1000 for ODF). One thing you notice when reading the DOCX spec is that they designed it with the sole constraint that DOC files could easily be converted to DOCX. For example, you'll frequently see compatibility tags like "autoSpaceLikeWord95", "footnoteLayoutLikeWW8", "useWord2002TableStyleRules", and "lineWrapLikeWor…
I expect that whatever tooling the USPTO uses can probably just ignore those things. They're extracting metadata, not actually rendering it.