CM tracking Vocabulary IDs, changing config store on sync

I am new to using configuration management, but here's what I've done:

1) set up a new site, create some content types and taxonomies.
2) Add the content types and taxonomies to configuration management, and export their configs.
3) set up a second new site, with the same config directory contents.
4) run drush csyn and/or synchronize through the GUI.

I get no errors, and on visual inspection it seems to have worked just fine. But Git tells me that tracked.inc, and several of the files in the configuration directory have changed.

If I delete the configuration directory and check it out again, the UI tells me that all of the tracked items are "synced".

The second time (maybe third?) I ran the sync operation, only the taxonomy vocabularies were changed in the config directory. That's when I diffed them and discovered the DB has different VID than the datastore.

So here are my questions:

* should "drush csyn" be changing ANYTHING in the config directory? I would expect not.
* why are we tracking VID if we can't guarantee it on restoring a configuration?
* is this a bug?