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As you suspected this may not necessarily be applicable to the patch KB you linked to above.
What does the directory structure of the source website look like? If you use the FTP credentials that you're using for the import process in an FTP client, what's the top level directory displayed?
I just tested this with another Plesk server. Had to disable FTPS. First it errors out and the extra two fields appear for directory and URL. I tried combinations of everything. Obviously on this test I was trying to drill into httpdocs.
The migration debug log might help - While a bit obscure and likely irrelevant, try checking to see if there are rewrite rules in the document root (i.e. look for instances of mod_rewrite in an .htaccess file) and try temporarily disabling the rewrite rules before attempting the procedure again.