Unlike Linux-based PPPoE/L2TP servers like accel-ppp, MPD5 does not support assigning IPv6 addresses outside of IPv6CP, unless you use a script to assign IPv6 to an interface and run a RA/DHCPv6(-PD) server.
I have a GitHub repo which has preliminary IPv6 assignment for MPD5 PPPoE/L2TP servers, but this uses the shell script and is incomplete: https://github.com/neelchauhan/freebsd-mpd5-ppp-ipv6
If you don't want to invent a IPv6 RA and DHCPv6 server, you could autogenerate rtadvd and dhcpv6 configs, but I don't know if that would be okay (considering you'd have 1000 rtadvd + 1000 dhcpd instances for 1000 clients).
I am attempting to add IPv6 hooks using the said approach on a fork: https://github.com/neelchauhan/mpdx
Keep in mind that this fork is far from complete and happens in my spare time, since my $DAYJOB isn't in networking or FreeBSD. And even in my free time I spend more of it on Ports being a committer myself.