Alright the reason that some rears dont matter and some rears you need to take apart or count the threads is because of whats known as a crush collar or crush sleeve.
What a crush sleeve does is set how much pressure is on the pinion bearings much like when you do wheel bearings and tighten the nut down.
The pressure or "preload" on the crush sleeve is set based on how tight the pinion nut/yoke is tightened. So when you remove the pinion nut and yoke to replace the seal you basically remove all the preload from the sleeve completely loosening the pre-load on the pinion bearings.
Now in order to fully understand this you would have to research the procedure for setting the pinion bearing preload. You would then understand why you cant "properly" set the preload again without installing a new crush collar and going through the proper procedure.
Now the incorrect or "shade tree" way to do it is to count the threads and mark the nut. That way when you re-install the yoke and nut you line it up with the proper thread count and give it another 1/8 o a turn and you're done.
The reason for this is because if you over crush the collar your bearings will be super loose and fail within miles.
Some rears, most danas, 14bolts I believe and some others have a solid spacer instead of a crush collar. You can easily tear the yoke off and retighten it down to a torque spec because the spacer is solid and uses shims much like setting up pinion depth or backlash to get the correct pinion bearing preload. Because of this the preload goes back to the same measurement everytime you torque the nut.
If I was vague on anything or you dont get it feel free to ask.
14 bolts use a crush sleeve, NOT shims. I wouldn't assume that Dana axles use shims, there are LOTS out there that use crush sleeves. GM D60's always use shims, however.

that exlpains the destruction of my rear end and i just slaped a rear yoke on my 14bff and used a impact gun!!!
...heres my rant why if anybody wants to read.... that probly explains why my pinion bearing worked its way into the pinion gear when i had a buddy do my gears. it did take a while when it happen...couldnt even tell it was ****ed up til it seized up....ended up destroying everything except main housing.... so i had a shop rebuild my entire rear end