@iBowler , To configure Enterprise Mode Site List with Microsoft Intune, there are a few steps to be involved:
-Create the Enterprise Mode Site list
-Create Azure Blob Storage
-Configure Administrative Templates profile in Intune
From your description, it seems we get some issue when Configure IE mode for Microsoft Edge. Here, we suggest to use Enterprise Mode Site list Manager with version 2 to get the EML. We can follow the steps in the following link to see if it can success.
https://www.inthecloud247.com/configure-the-enterprise-mode-site-list-with-microsoft-intune/
Note: Non-Microsoft link, just for the reference.
Hope it can help.
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