My opinion.................mount it on top, the way that Yamaha engineers designed it to work. These are brakes you are talking about, so safety is a major concern.
Well, now we are getting into a dangerous area...A caliper on top will put the static brake stay in compression, which again may cause buckling in the stay. So the stay will need to have sufficient bending stiffness for its length, in order to be safe.
An underslung caliper arrangement will put the static stay in tension, so stiffness is of no concern. The stay can be a steel rod with uniballs at the ends, for example.
An underslung caliper mount is perfect for use with a drum brake swing arm, as the lug is at the bottom. With the stock disc brake swing arm, the lug is on the top, and I WOULD STRONGLY RECOMMEND TO USE THE STOCK STATIC BRAKE STAY
Also, the Brembo 2-piston rear calipers come in 2 versions, so the bleed nipple stays on top both for top mounted and underslung calipers.
If one decides for an underslung caliper, it is important to locate the lug for the brake stay as far away from the wheel axle as possible, for best leverage/ lowest load. And the stay and a line from lug to wheel centre should form a 90 deg angle, again to minimise loads.
If not familiar with structural/ mechanical engineering, please seek advise from someone who is, when it comes to brake modifications.