pfSense

Yes, I was thinking a similar thing. "Allow IPv6" is really meant to be a general blocker for outside things that might be hitting the firewall with IPv6 - it is a safety-net/comfortable/feel-good thing to turn off on systems where people are not yet at all ready for/comfortable with/understanding IPv6.
There should be no issue letting the firewall talk to itself with IPv6 at all times.
Maybe change the description to "Allow external IPv6" and modify the long text to say:
"All external IPv6 traffic will be blocked by the firewall unless this box is checked."

Anyway, entirely up to you - I have no special preference there.

I'm still seeing NTP IPv6 requests blocked on lo0 using the Sat Dec 13 13:26:22 amd64 build. Should this fix be present there?

See https://forum.pfsense.org/index.php?topic=85372.

So far, all that has been committed is a change to the ntpq command that gets the ntpd status, forcing it to use IPv4 when IPv6 allow is off.

ntpd is still doing the same as it did before, using whatever IPv4 and IPv6 it finds or is configured to use. I guess the firewall is talking to itself here to find out the time. This is 1 example of internal processes that are talking to each other using IPv6 sockets. The user could work around it by disabling logging on the "hidden" default block all rule, then for things they want to block and log, put their own block and log rules on interfaces where they want to have the logging.

Chris can decide about whether to modify the default blocking rule so that there is an allow for the firewall to talk to itself, or to modify ntpd behaviour so it only uses IPv4 when IPv6 allow is off, or...

Well noted Andy, the pass was not having effect. It needs "quick" on that pass rule.
Pull request: https://github.com/pfsense/pfsense/pull/1419