When I'm trying to run a script using nix-shell, $PATH contains several folders starting with coreutils from standard environment:

$: nix-shell --packages darwin.shell_cmds --pure --run "echo \$PATH"
/nix/store/s28xb9v7xf6axvf4a3av2mnczws2hsdg-coreutils-8.29/bin:/nix/store/j2z3v4g8y39ph0z03mh2cv2xaqvfmrai-shell_cmds-osx-10.11.6/bin

Unfortunately, since coreutils is in front, it will be looked into first. That means, in case of a conflict, binaries from coreutils will always be picked.

In the case above, shell_cmds contains mktemp for Mac OS which is slightly different from GNU's one, but there is no easy way to make the script inside nix-shell to use mktemp from shell_cmds.

I think a solution here is to always put packages defined by user in front of the PATH and put all the default stuff in the end.