pfSense

Point 1 isn't relevant -- that has no effect on anything other than the firewall rules being able to pass IPv6, it does not disable anything at the networking/stack level.

The actual issue appears to be that the "DNS Resolution" option has no effect on pools, only peers and servers.

It appears to work by adjusting the code to hit both paths, but could use some more testing. It's possible it wasn't supported by ntpd in the past when that option was added initially.

You can try applying the following diff (ignoring whitespace) in the System Patches package:

diff --git a/src/etc/inc/system.inc b/src/etc/inc/system.inc
index c7549317c4..bb0a785667 100644
--- a/src/etc/inc/system.inc
+++ b/src/etc/inc/system.inc
@@ -2538,11 +2538,11 @@ function system_ntp_configure() {
                        } else {
                                $ntpcfg .= 'server ';
                        }
-                       if (config_get_path('ntpd/dnsresolv') == 'inet') {
-                               $ntpcfg .= '-4 ';
-                       } elseif (config_get_path('ntpd/dnsresolv') == 'inet6') {
-                               $ntpcfg .= '-6 ';
-                       }
+               }
+               if (config_get_path('ntpd/dnsresolv') == 'inet') {
+                       $ntpcfg .= '-4 ';
+               } elseif (config_get_path('ntpd/dnsresolv') == 'inet6') {
+                       $ntpcfg .= '-6 ';
                }

                $ntpcfg .= "{$ts}";

Applied in changeset 26a06fbad188a772f862c830d3918fb5588a2002.

Jordan G wrote in #note-5:

the info/tip below NTP's DNS resolution option currently states it has no affect on pools. This should be updated if it now does change pool name resolution.

Fixed in 5ae3f26433ce76d5b238f610ac734fa7a9aa07a5