I don't see much of an issue with what you're trying to do. Just make sure your "primary" package is your base package, and that all of your plugins declare a runtime dependency on that primary package. Also, make sure that there aren't any paths that overlap among packages relative to the build root $PREFIX. There's a configuration parameter than can help with that.
# path_conflict (PathConflict)
# The method by which conda handle's conflicting/overlapping paths
# during a create, install, or update operation. The value must be one
# of 'clobber', 'warn', or 'prevent'. The '--clobber' command-line flag
# or clobber configuration parameter overrides path_conflict set to
# 'prevent'.
#
# path_conflict: clobber
Someday conda's default value will start to become more strict, moving to warn and then prevent. Path conflicts can cause some surprising, unexpected, and basically just really bad behavior.