You can change the actual material dimension with no issue (length/width) , but it's not really necessary as long as the stock you use is at least that size and you properly center both to the same center reference point. That's why I recommended the locator pins on the centerline so you can flip things over. As long as the center point on the model stays in the same place for both, you'll be fine.
I don't recall the material being different thickness on the files I received. Both were 20.74mm thick. (or whatever the Imperial equivalent is...I work in metric most of the time) If you got files where the top of the neck "includes" the fretboard, you're going to have to manually calculate the difference with the fretboard removed. My files are the 1962 Telecaster version, but for the P-Bass files, he had the fretboard included in the neck top file and I had to do some faddling with math. Based on the dimensions you mention, it does seem the case that the files you have may have the fretboard integral as the Fender specification for final fretboard thickness (when cut separately) is just under 5mm. (about .2 inch)
One other note...the files you have likely are setup to measure from top of material. If that's what you use on your CNC machine, no problem. I have to be sure to remember to switch them to measure off the machine top for my particular setup because I have automatic tool measuring. If I forget to make that change if I open the original file, the result is, um...not pleasant.
Whenever you obtain files from someone else, check out the defaults for material size and measuring point carefully to be sure it's appropriate for how you work.