Under iOS 10 (and 11) an External Accessory application which supports the protocolString registered by an accessory is always autolaunched when the accessory is attached. I suspect that your accessory uses the iAP command to request the launch of the matching application when the accessory is connected. The use of the iAP command will cause the requested app to come to the foreground when the device is unlocked. The iAP command has no effect when the device is locked. However, the app is still autolaunched. The fact that you report transfer activity on the accessory side tells me that the UIBackgroundMode property is set with "external-accessory".
If you wake the device after the app has been autolaunched, you may find that the application is not presented in the app picker UI. This is because the UI was not used to launch the app.
rich kubota - rkubota@apple.com
developer technical support CoreOS/Hardware/MFI