Of course Auto Exposure
adjusts the exposure, as the exposure
changes. That's the whole point! Unless you lock it, which you can
also do. If the exposure varies, and you are adjusting it
manually to maintain ISO 100 and the appropriate shutter speed, as
@msinger was suggesting above, you will still be
manually jumping by 1/3 stop intervals. No difference!
ND filters do NOT reduce the
dynamic range of the scene, as you seem to believe. They
merely reduce the amount of light. It's this sort of misinformation that results in everyone buying unnecessary ND filters, when what they
really want, if they understood the concept, are
Graduated Neutral Density filters, which DO reduce the dynamic range of the scene. If you use a
GND filter late in the day to keep the sky from blowing out, as it gets darker, after sunset with Auto ISO, you can get a linear change in exposure in the ISO increase, rather than jumps of 1/3 of a stop.
BTW, if nothing is
moving in your scene, there is no point in using an ND filter to create a motion blur, as the video which
@msinger cited above, explains. Watch it.