With the latest updates on Intune, you can now define specific users/devices when you apply a Windows Hello policy. Until then, the Windows Hello policy was a tenant level settings and as such applied to all users/devices.

To define the Windows Hello policy, go to your Intune configuration blade and reach out the Device configuration\Profiles and create an Identity Protection profile, then you will be able to define the targeted users/devices by defining the Assignement

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