When I ran 5/3/1, I did more assistance work because I like lifting and the program is very minimalist.
I'd do incline bench, flyes and rows on bench days
Leg press, hack squat and leg extension on squat days
Machine presses, dumbbell laterals and rear delt flyes on press days
Good mornings, hamstring curls and abs on deadlift days. I would sometimes throw dips into one of the press days for variety.
I saw good strengths gains and felt like I did enough at the end of every gym session.