You can't directly compare the images then.
You may find that the quality of the images may vary to what you currently see in them.
processing them can introduce quality degradations.
All the exposures should be captured to the same exposure level .. or as close as can be.
So if you had a 3 stop ND attached then of course shutter speed should be the variable you slow it down by 3 stops compared to the non filtered exposure.
As you've noticed yourself filters don't always work the way they're rated too. So it's handy to know if you 8 stop ND is actually 8 stops worth or is it really only 5 or something.
Sounds more like a variable ND, not graduated ND.
Grads are the ones with half dark, half clear graduations to balance uneven exposure scenarios.
The NDs that darken as you rotate the filter's ring are called 'variable'.