I think I've figured this out;
The standard download for 18.104.22.168 has the option for IPv6 in the Admin properties, but it cannot be activated. I needed to use the dedicated 22.214.171.124 IPv6 download which contains the viewer and winvnc.exe.
When I overwrite the installed winvnc.exe and start the service, I now can enable IPv6 (tested over DirectAccess, it works!).
Much like Olav, I need to figure out a way to dynamically choose IPv4 vs IPv6. Since on DirectAccess we can only do reverse VNC connections, I think I'm going to do the following:
Provide a shortcut on the desktop for "IT Remote Access", which does a lookup to the registry key Olav mentioned. If that hostname resolves to IPv4, simply run "winvnc -connect". If it resolves to IPv6, then modify the line for UseIPV6=1 in UltraVNC.ini, start and stop the service, and run "winvnc -connect".
Cumbersome, but this way as our staff roam inside and outside the office, IPv6 will only be enabled when they request support.
If UltraVNC could dynamically support both protocols at once like TigerVNC that would of course be ideal.