Out of curiosity which vehicles have you heard use PWM?, as i professionally kit up pedal controllers and have yet to see them in Mitsubishi, Toyota, Hino or Isuzu (well there is one odd model of Mitsubishi but I call that an anomaly,as its not pwm but AC coupled data on the analog signal)
equally my comment about using a low pass filter is almost exactly what will be on the ECU side of the pedal controls, and will still get you the voltages necessary to replicate with your own controller, to test for yourself hook your multimeter up to mains on DC volts, it will read very close to 0V, and this is only a 50/60Hz signal, where as any vehicle PWM would be at-least 500Hz to be reliable and not jump about from averaging, meaning as-long as its faster than mains be it a post true RMS or a $5 El-crapo cheapie meter its reading should be very close to the average and more than enough to give you the info you need,