I've noticed that the hilite_pet option rests to false upon restarting, but other options such as autodig, pushweapon, etc., that I set at initiation stay as set. Is this a bug that can be fixed?
Some options appear to be tied to the character, like pushweapon, and get saved with the character. This setting can be fun early game or, for classes that don't duelweapon, even late game; but just trying to play a duelweapon character with this setting on will drive you nuts. These may change with your play style between characters, particularly if you're the type of person who will likely have a couple active saves available to suit your mood.
hilite_pet on the other hand is more of a User Interface choice, and is best set in a .nethackrc or defaults.nh file. This is the kind of thing you'll want to be the same in every run.