Even though Microsoft Docs lists Microsoft Update as supported cloud sources (https://docs.microsoft.com/en-us/configmgr/core/servers/deploy/configure/boundary-groups#bkmk_bgoptions4), "Prefer cloud based sources over on-premise sources" does not seem to apply to Microsoft Update content in the case of an AlwaysOn VPN scenario where devices would show in "intranet" all the time.  
The only alternative option is splitting up update deployments (VPN vs Non-VPN) and working with the download settings on the individual deployments, which is very cumbersome. If a client falls into a boundary group which has the setting enabled, it should respect it and use Windows Update for source content.