I'm surprised that nix never ended up using augeas for package configuration because last I checked every upstream build option has to be reproduced in nix script by the packager.
It's easy enough for users to extend existing packages in Nix that it's never necessary for packagers to explicitly add support for every conceivable upstream build option out there. For example, the following three lines will create a new package based on an existing one with custom configure flags added.
Package options that tweak the build flags are there for convenience and not a requirement. Many of them are there for internal use in the Nixpkgs repo to provide variants of the same package.