The "The phpMyAdmin configuration storage is not completely configured, some extended features have been deactivated. Find out why. Or alternately go to 'Operations' tab of any database to set it up there." error is shown on home even though I've got pMA tables in one of the DBs (via ZeroConf).
It seems to not detect this until I visit this DB.
Indeed, this is not a covered scenario for ZeroConf. Again, the recommended way is to properly set up the configuration storage.
It would not be efficient to try to detect in all databases the presence of the configuration storage, and IMO not efficient to clutter each database with an instance of the configuration storage tables.
The pro of having the pMA data together with the normal data is that it's automatically included in backups (and restores).
Scheduled to be discussed at the next team meeting:
https://wiki.phpmyadmin.net/pma/2015-02_Meeting
maybe somthing woring with phpmyadmin configration file
Fixed with https://github.com/phpmyadmin/phpmyadmin/commit/0f720c53752e260e4384f8172c4501c5aba30088