I'm experiencing the same thing. When I run the security cms -D -i /path/to/your.app/embedded.mobileprovision command I see <key>Entitlements</key> <dict> <key>aps-environment</key> <string>development</string> ... However, running the codesign -d --entitlements - /path/to/your.app command, there is no aps-environment Key. Just to be sure I was looking for the right thing, I ran the code sign command on another app that has Push Notifications working, and the aps-environment Key is present there. It seems that something in the build process is causing this issue. Now to dig into that to see if anything sticks out.

Following up - While the "Automatically manage signing" option is enabled in Xcode, I did have a provisioning profile for this app in developer.apple.com that was generated before I enabled Push Notifications. I deleted that profile and created a new one now that Push Notifications are part of the app, toggled Automatically manage signing off and then back on, and the next time I built the app, the aps-environment issue was resolved and a push token was available. Hmm.