Thanks, that helped to find the issue! In the trace log I noticed an access to fuse-overlayfs outside the nix store.
Apparently, I had some configuration files hanging around in ~/.config and ~/.local, from a previous Fedora installation. I just dropped those and things and it works now.
I don’t know why it uses fuse-overlayfs instead of native overlayfs, but it seems to do so even after I removed the old configurations.