In case you haven’t seen it, at Ignite in September we introduced the concept of co-management with Configuration Manager and Intune both managing the same device. https://channel9.msdn.com/Events/Ignite/2016/BRK2138-TS
If you already have ConfigMgr, it makes sense for now to consider this configuration to address app deployment.
204 votesPaul commented
I also want this improvement. Plus not only for autopilot but also for devices that ain't rolled out with autopilot.
You can get the policy using the Graph API, which is even better because then you can script it to set the policy in another tenant. Would that get you what you want? Or is it an actual button you want?