You have to build up a list of items for syncing anyway, so an exclude list was possible. In case of manual includes especially for directories a exclude list may be handy too.
The scm-sync-configration plugin was on the way to be a save and recovery tool for Jenkins configuration, so it should be possible to fine tune the content synced to scm.
A fixed white list probably requires maintenance for every change/addition of plugins and core.
An exclude list gives the responsibility to the administrator and no white list have to be maintained anymore.
This will make the plugin more flexible.
Exclude lists give an administrator the freedom to save only what he need for his purposes, e. g. save only several job configurations and plugin settings.
This may be needed if there are temporary or not common jobs and plugins are used on a Jenkins server.