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I was experiencing the same, and got around it my adding the permissions I needed manually to the manifest on the App Registration. To retrieve the IDs I just copied them some a similar App Registration I had on the Public Cloud. After doing so, they showed up properly under the Configured Permissions as "Office 365 SharePoint Online" permissions and they worked correctly in my client application.

For example:

"requiredResourceAccess": [
        {
            "resourceAppId": "00000003-0000-0ff1-ce00-000000000000",
            "resourceAccess": [
                {
                    "id": "c8e3537c-ec53-43b9-bed3-b2bd3617ae97",
                    "type": "Role"
                },
                {
                    "id": "20d37865-089c-4dee-8c41-6967602d4ac8",
                    "type": "Role"
                }
            ]
        },

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