The problem seemed to stem from not signing the archive (CODESIGNINGALLOWED=NO is bad in this case). Once the xarchive was signed with the provisioning profiles then I no longer received the email from Apple after uploading.
I'd originally avoided signing the archive because I'd struggled to get it working with more than one provisioning profile but eventually found the following solution: https://stackoverflow.com/a/29605731/2520623
For reference, this is what my final archive command looked like:
xcodebuild -sdk iphoneos -configuration Release -project myapp.xcodeproj -scheme MyApp archive -archivePath myapp.xcarchive -allowProvisioningUpdates OTHER_CODE_SIGN_FLAGS=--keychain tempkeychain.keychain APP_PROFILE=[UUID of app's prov profile] EXTENSION_PROFILE=[UUID of extension's prov profile]
benjfromlondon
Users receive reputation points by contributing quality content to the forums.
Posts include post and replies published on the forums.
Post authors can mark replies as Accepted to indicate successful solutions.
Apple Developer Forums admins can mark replies as Apple Recommended to indicate an approved solution
Last seen
User for
Post
Replies
Boosts
Views
Activity
It looks to me like the Leaks Instrument times out before the app fully initialises. A workaround for this seems to be to start Instruments from within Xcode once the app is running.
In other words; start the app in Xcode, go to the Debug Navigator, click the Memory item there and then in the main window click Profile in Instruments (top right). That should take you right into the Leaks Instrument running against your app.