[Andrew]

OmniFocus for the Mac never automatically cleans up the Inbox - you have to manually invoke it via the Clean Up item in the Edit menu or by clicking the Clean Up item on the toolbar.

OmniFocus for the iPhone automatically cleans up the Inbox when redisplaying (when changing views, for instance, or when refreshing from synced data). By default it will clean up any item that has either a project or a context assigned, but when syncing with OmniFocus for the Mac it will adopt the behavior configured in the Inbox Processing section of the Data preferences in OmniFocus for the Mac.

So when your Inbox items from the Mac get synced over to the phone, they get immediately cleaned up if they can be, according to the Inbox Processing settings. (And then when synced back to the Mac, that is reflected on the Mac as well.)