Apple's Mobile Device Management Protocol Reference states on page 44 at the bottom
Third-party enterprise applications require provisioning profiles in order to run them. You can use MDM to deliver up-to-date versions of these profiles so that users do not have to manually install these profiles, replace profiles as they expire, and so on. To do this, deliver the provisioning profiles through MDM instead of distributing them through your corporate web portal or bundled with the application.
Does this mean that I should remove or unbundle the embedded.mobileprovision from the application before installation?
Or does it mean,
Installing the provisioning profile via an MDM server separately before installing the app?
If the answer is the first one, how does one remove the embedded.mobileprovision without breaking the app. If the answer is the 2nd, does subsequently updating the app mess up the profile installed by the MDM server?