@Michael Hailemariam, Thanks for posting in Q&A.
Currently, Intune only support the Linux Ubuntu Desktop with a GNOME graphical desktop environment. For the server without a graphical. I am afraid It is not supported yet. You can feedback in the following location to see if it can support the server only with command line in the future:
https://feedbackportal.microsoft.com/feedback/forum/ef1d6d38-fd1b-ec11-b6e7-0022481f8472
Thanks for your understanding.
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