With Wireguard you set DNS server IP directly in the config file, it is not negotiable over the connection. So you can edit the config to set it to your pihole'

With Wireguard you set DNS server IP directly in the config file, it is not negotiable over the connection. So you can edit the config to set it to your pihole's ip. Or remove the DNS line altogether and then it won't touch your DNS settings at all.