When using Cisco OpenConnect client there are no problems resolving IPv6 only sites. However while using open source openconnect command line client from brew Safari can't resolve IPv6 only sites. Open source openconnect uses vpnc script to configure network interfaces. IPv6 address is assigned and connectivity is working just fine.
Same problem with OpenVPN, both open source and proprietary OpenVPN.net client.
While searching for an answer I came across a question first posted on apple communities exactly three years ago: https://discussions.apple.com/message/24511921 but it does not provide any command line solutions suitable for adding to vpnc script.
Are here any scutil experts? I suppose there should be away to mark a VPN interface utun0 as IPv6 enabled. At least official Cisco OpenConnect client somehow does it just fine.