I am using WireGuard on my iPhone, and the endpoint is specified by a
domain name that has both AAAA and A record. When I turn on WireGuard
in a network with dual IPv6 and IPv4, I find out that WireGuard
chooses IPv4 by executing "wg" on my server. If I explicitly set the
endpoint as IPv6 address, WireGuard works just fine, so it is not a
misconfiguration on my server.

Most operating systems prioritize IPv6 over IPv4, so it is baffling
why WireGuard iOS goes the other way. More importantly, this is not a
theoretical discussion for me: in my case, IPv6 has better performance
due to less congestion (as fewer people utilize it). I also have an
IKEv2/IPSec VPN configured on the same server, and it performs better
because it always prioritize IPv6.
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