I warned you it was anal. Pertains to any bike with a chain. Sometime when you're really bored drop your shock and choose your own reference point so you never have to wonder where to take the measurement.. It's pretty much the only way to guaranty you won't tear anything up.
I realize that hardly anyone is gunna do it, but any time you change sprocket ratios, lengthen a swingarm, lower or lift the rear of a bike the ratio at which your chain slack becomes critical changes. It also determines the limits of how much you can lift/lower a TW (or any other bike with a chain for that matter) before you'll need a tension roller, and another reason to rethink that Blaster shock swap. This is also how manufacturers determine proper chain slack to print in their manuals.
The other reason I do it is because YAMAHA wrote our manual. Just sayin'. I'd highlight all the incorrect info in that manual but I'd run out of red ink.
If you're going to use the manual's spec the correct location for taking the measurement is the middle of the entire bottom run of chain. A lot of people mistakenly use the middle of only the visible part of the chain run or the middle of the swingarm as a reference point.