I find allowing the shy regexp to match zero or more times
(using a '*' instead of '?') solves not only the use case of
including -S as an option, but also can support other options to env.

I have this now in my init.el:

(setq auto-mode-interpreter-regexp
;; support -S and other options to /bin/env.  See
;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=64939
  (purecopy "#![ \t]?\\([^ \t\n]*\
/bin/env[ \t]\\)?\\(?:-\\{1,2\\}[a-zA-Z1-9=]+[ \t]+\\)*\\([^
\t\n]+\\)"))

Hooray?

Why not patch lisp/files.el accordingly?

~ Malcolm Cook