The normal use case for Machine Tunnel works something like this:
- User boots computer
- Machine tunnel is established in the background
- Once user authenticates to Windows and logs in, VPN client terminates the Machine Tunnel and is switched to a User Tunnel
At no time is there both a User and Machine tunnel active.
Also, the User and Machine tunnel are expected to be with the same gateway (not a different one) with "Always On" configured.
In your specific case, "Configured on Endpoint Client" would allow the checkbox for "Always On" to be configured on the client, whereas "Manual" requires the end user to activate the VPN connection.
Note that any changes to Global Properties affects ALL gateways managed under the domain.