L293 DC Motor Driver : How to set up PWM
Driving the EN pin in PWM while driving A1 and A2 in opposite directions will provide the desired speed control as you had originally planned. To create a full stop you can drive both control pins low while keeping EN high. This will act as an electric brake by shorting the motor to itself through Gnd.

Using A1 and A2 in opposing duty cycles would also work on paper, but this is really creating a tug of war effect where the motor is being driven backwards rather than having a real "off" PWM state.

As an illustration: if your PWM frequency was unreasonably low (like 1Hz) you would see the motor run back and forth, but it would eventually trend in one direction in a "two steps forward, one step back" pattern (not ideal). Also if the 50% duty cycle is not perfectly balanced (or if there is driver imbalance inside the IC) you will see the motor creep in one direction rather than stay stopped.