You misread that. He wasn't saying that dbfiles are better than BerkeleyDB. It would make little sense to say that since BerkelyDB is nothing more or less than a specific kind of dbfile.

Instead he said that in the case he described, BerkeleyDB would be a bad choice. In other cases a dbfile would be a good choice. So it is all about why different cases make a different difference.

For your problem a dbfile is a reasonable choice. But I'll note that if you can you really want to pre-sort your data then store it in BTrees as much as possible. That will massively improve your locality of reference, which will reduce disk seeks. And I guarantee that with that problem you're being killed on disk seeks.