I mentioned the 2 command line programs to remind you of their existence - only you can determine if they're relevant to your workflow.
As far as I can tell PDF XChange can display the xmp metadata, see File->Document Properties->Additional Metadata->Advanced. The DC elements are in the
http://purl.org/dc/elements/1.1 section. But I don't think it can change or add new elements directly. Given PDF and XMP are Adobe creations I would assume one or more of their tools can populate any DC element in the EPUB.
I'm not sure if calibre reads the XMP data in the PDF when its adding books, why don't you do a test
- add some Identifiers to a library book that has a PDF,
- use calibre Embed Metadata (ctrl/e) to embed the metadata in the book,
- verify it's there with PDF XChange,
- save the PDF somewhere,
- delete the book from calibre library,
- add the saved PDF with Add options set to extract metadata from file
Are the Identifiers there?
I think Calibre will embed custom columns as XMP in an PDF, in a calibre section. But I don't know if it will read it back when a book is added - I suspect not because everyone's custom columns are different. Again why don't you try it out.
If you were to put your version number into say the Title eg "Robinson Crusoe : Version 123" then after adding books you could use Bulk Metadata Edit: Search and Replace: Regular Expression facilities to extract the version number from the Title, put it in a custom column and remove it from Title - S&R definitions can be saved, to facilitate reuse. That's how many (most) people tackle this sort of issue.
BR