Now having a proper way to test this, I've come across a major bug: BungeeCord cannot pull from the server map! This has been fixed.

For reference, this version does not show up in the timeline on the GitHub page as the next version is already in development, however since SubServers.Sync 2.13a (beta) is slated to not be compatible with SubServers.Bungee 2.12.2f this patch was released for those not yet ready to update.