One thing to remember, and one of my pet peeves...
Out of all of the files in ~vpopmail/domains/example.com/ only one,
.qmail-default has anything to do with the vpopmail delivery process.
When qmail-local tries to deliver a message to the domain it looks at
all of the .qmail-* files in the domain directory, and processes the
.qmail* file that best matches the incoming address. If no other .qmail
file matches .qmail-default is processed, which is where vdelivermail
see: man dot-qmail
.qmail files in ~vpopmail/domains/example.com/username will be handled
by vdelivermail depending on compiler options.
Vpopmail and qmailadmin do manage the .qmail files in the domain
directory, but during the delivery process qmail does not pass control
to vpopmail unless none of the other .qmail files match.