This setup has now been working very well for the last two weeks: dump1090-mutability_1.15~dev, and piaware with its faup1090 & fa-mlat-client as built by piaware_builder dev branch.
All three (dump1090-mutability, piaware and fa-mlat-client) now use IPv6:
dump1090-mutability --net-bind-address ::1 ...
piaware -serverhosts hullo.hou.flightaware.com ...
piaware is able to talk to hullo.hou.flightaware.com over IPv6,
faup1090 is able to receive data from dump1090 over ::1]:30005,
fa-mlat-client is able to talk to dump1090 over ::1]:30005 and ::1]:30104,
and to fa server over IPv6 (–udp-transport)
There is still one detail that needs fixing: during piaware startup when it is deciding whether to start fa-mlat-client or not, it checks if a dump1090 is present on port 30005. The dump1090-mutability is listening on 30005, but is bound to ::1 and not to 127.0.0.1, so piaware decides there is no dump1090 and refuses to start fa-mlat-client:
piaware version 3.0~dev is running, process ID 13263
your system info is: Linux sleepy-rpi3b 4.4.7-v7+ #876 SMP Tue Apr 12 22:28:41 BST 2016 armv7l GNU/Linux
...
Connecting to FlightAware adept server at hullo.hou.flightaware.com/1200
Connection with adept server at hullo.hou.flightaware.com/1200 established
FlightAware server SSL certificate validated
encrypted session established with FlightAware
no ADS-B data program seen listening on port 30005 for 3 seconds, next check in 60s
logged in to FlightAware as user xxx
multilateration data requested
no ADS-B data program is serving on port 30005, not starting multilateration client yet
0 msgs recv'd from dump1090; 0 msgs sent to FlightAware
no ADS-B data program seen listening on port 30005 for 63 seconds, next check in 60s
no ADS-B data program is serving on port 30005, not starting multilateration client yet
Nevertheless, if fa-mlat-client is then started manually (with the same arguments as when piaware would be starting it, e.g. --udp-transport 2600:c13:1002:4::191:ppp:nnn), it does work and does communicate with hullo.hou.flightaware.com over IPv6.
So the only problem is that piaware does not see that dump1090 is listening on ::1]:30005, as it only checks its presence over IPv4.
As a workaround, I can use haproxy which proxies ::1]:30005 to 127.0.0.1:30005, so that port 30005 is reachable over both protocol families. Note that after a piaware is up and running with both its child processes, the haproxy can be turned off and everything continues to be running normally.
It would be nice to solve this missing detail eventually, for a truly IPv6-only setup.