Store Automatically Currently ignores the settings in the selected store dialog. It should still default values in fields etc.
Personally I think this is a bug. Currently Store Dialog settings like preloaded default values are ignored. If you select multiple documents in a tray and use the Store Automatically the settings of the store dialog are not processed. This causes huge issues if a status field for instance was preloaded to kick off a particular workflow. The user is allowed to do it but the documents get stored without the necessary default index values and the user has no idea the fields were not filled in as they are if they store one at a time with the store button.