This is Tor Control panel bug and is unrelated to Qubes. I’ve tested it with Whonix on KVM and it fails in the same way.
I’ve found a workaround:
If you add at least one obfs4 bridge in you config in Anon Connection Wizard and add your other bridges with transport ‘none’ then the Tor Control panel can be started and used again.
UPD:
It seems that it’s enough to just add ClientTransportPlugin in torrc config and it works even without adding obfs4 bridge:
sudo sh -c 'echo "ClientTransportPlugin obfs4 exec /usr/bin/obfs4proxy" >> /usr/local/etc/torrc.d/40_tor_control_panel.conf'
Also it doesn’t work if I add ClientTransportPlugin /usr/local/etc/torrc.d/50_user.conf.