Thanks for your message.
In the meantime, I figured it out with the help of one member of Atlas support.
Turns out that it’s impossible for an atlas cluster on GCP to reach a private endpoint (our LDAP) through a VPN connection (cloud VPN).
This is because the peering between the atlas GP project and our GCP project does not accept our custom routes so no hop is possible for the atlas cluster to reach our LDAP.