@Lance Lingerfelt, Thanks for posting in Q&A. Based on my testing, I have enrolled one windows 11 device into Intune. And find the remote desktop is on.
For your issue, it can be that some policies applied to this device block the remote desktop feature. to check this, you can find one affected device, check the device configuration policy applied it and see if any has setting related with remote desktop:
Please check the above information and if there's any update, feel free to let us know.
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