SUMMARY:
If you open a project in Xcode 8 with \"Automatically manage signing\" enabled and a new bundle ID, it will automatically create and download a
As far as my understanding and recent readings, the answer to OP's question:
"Can xcodebuild manage automatic signing?" is "YES" but not as per the OP's expectations in lines of "when you haven't created the app ID or provisioning profile yet, and you want to create it automatically the way Xcode does"
As per this informative blog on xcode8 and automatic code signing, it clearly states that :
"If you want to create for example an App Store signed IPA, on the Mac you have to have both a Wildcard, Team / Development AND the App Store distribution certificates and provisioning profiles!"
Hence, the app ID and provisioning profile wont be auto created. Fastlane may be a workaround to this problem but i guess that is not the OP's expectation. Hope it makes sense.