Yes, you're right - I lazily linked to the original project.

However the new project has the same issues with DNS over VPN on FreeBSD. I have personally corresponded with the current maintainer, etc., and since they build and test only on Linux, it's not something that ever got fixed.

If you read the original HOWTO/README from the original project, it details the issues and I can confirm that no amount of settings changes or workarounds will allow you to get DNS over the tunnel on FreeBSD.