Following the release of the latest version of System Center Configuration Manager (SCCM) Current Branch, 1910, also known now as Endpoint Configuration Manager (ECM) Current Branch 1910 (see https://t.co/ac1nnORrrN), you can enable support for Windows 10 Multi Session (aka Windows Virtual Desktop) by enabling the setting in the SCCM Client Settings\Client Policy
This will allow you to manage your Windows Virtual Desktop environment using SCCM.