For these types of sites we run a local CA, and sign regular certificates for these domains and then distribute the CA certificate to our windows clients through a GPO. When put into the correct store, all our "locally-signed" certificates show as valid.
In other instances, where I haven't been able to do that, like for disparate VPN clients and such I will generally assign a RFC1918 address to it. Like service.vpn.ourdomain.com resolves to 10.92.83.200. As long as I can respond to a DNS challenge, I can still get a letsencrypt certificate for that domain.