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}";