This is caused by the autoconf check for nix-store which is equivalent to running this:

$ nix-store --timeout 123 -q

This would open the pager on a 2.1.1 version of nix.

$ nix-store --version
nix-store (Nix) 2.1.1

Setting PAGER to cat ensures the pager doesn't block the configurePhase.

$ PAGER=cat nix-store --timeout 123 -q