Why is measuring horizontally cheating? Surely it is this dimension that is most relevant (position of vertical rider weight relative to tyre contact patch). Isn't this the dimension that influences the (mythical and much debated?) short chainstay / weight on the back wheel traction?
Measuring along the chainstay is only really useful for working out singlespeed wheel position / chain length / gear ratio combo.
And does it make much difference how you measure it anyway? I'm playing with a design for my own consumption (just about to order a pile of tubes). 29er ss, super short stays, slack-ish front and short rigid fork. Stays come in at 16.05" along the chainstay or 15.83" horizontal (so less than a quarter of an inch difference no matter how you measure it). And before anyone asks it does have mud clearance with fat tyres and regular crank spacing!
It will probably handle like a bus but who cares - if I don't like it then will just buy a few more tubes, melt apart the bad bits and try something else!
Carve your own niche.......