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Yes..what you are measuring is the force it takes to turn the shaft..this is the friction of the bearing loading. That has a spec so that the pinion does not move lateraly when power from the engine is applied.
An easy way to invision this is a simple/generic front wheel bearing adjustment...as you tighten the WB nut , the wheel gets harder to hand turn..that is bearing load. Too much and you burn up the bearing, too little and you have a loose wheel.

So, if you measure the needed force to turn/rotate the pinion before dis-assembly, you know where you have to go when you put it back together. It is the final in/lb reading you are concerned with..regardless of what it takes, be it 125 ft.lbs or 165 ft/lbs , on the pinion nut to get there ,it takes what it takes. If you just used a set torque in ft/lbs on the nut, you would have no way of converting that into bearing load , as every case would be different.. That is why CH said Small Increments as you approach the correct in/lb loading spec. So you tighten the nut and then take a reading each time until you get the proper in/lb reading. There are factory specs for this if you do not want to use the original that you had before dis-assembly.
The problem can arrise if one where to go to far b/c you can not loosen back..that is the trick.
And that is why most guys just index the pinion nut and put it back where it was originally..the problem with that is you don't know if a guy was in ther before you at some time, but if the diff has been fine except for the seal, it is a good guess that all is OK.

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A Dalton