hydraUnstable should enable flakes
Currently using hydraUnstable with flakes causes evaluation errors unless flakes are enabled system-wide. This in turn causes a lot of warnings to be emitted by regular nix commands if the system does not use nixUnstable.
As hydraUnstable internally uses nixUnstable, it would make sense that it also enables flakes locally. This can be done by creating /var/lib/hydra/.config/nix/nix.conf with the following content:
experimental-features = nix-command flakes
IMO the Hydra module should do that automatically when it sets up /var/lib/hydra/.
To prevent subtle regressions from slipping in from the Nix side of things, it probably should be an option that defaults to off.
There has been too much breakage around Nix 2.4 and assumptions that nix-command and flakes are turned on.