Hi David,
Robert is right, the pattern version is hardcoded.Taking a glimpse at the patterndb v3 and v4 XSDs I think the update should indeed be trivial, the format is upwards compatible. I'll send a pull request for this change in a minute.
Regarding the formatting: it uses the parsing mechanism of syslog-ng internally. It works just as if you specified a file() source for syslog-ng with flags(syslog-protocol) added. You can also give "--no-parse" for the tool which makes it parse logs just like a file() source with flags(no-parse). It wouldn't be too complicated to make it possible to use all available file source flags but I never got around doing it.
cheers,
Peter