FWIW, I was able to copy the SELECT_WINDOW_EVENT code from X (xterm.c) and Win32 (w32term.c) into nsterm.m, adjusting for a few minor differences in variable naming. Focus-follows-mouse on windows within the active frame when mouse-autoselect-window is not nil now works fine in my (not extensive) use of Emacs on my computer. Patch attached.

Davor