My front brake was set up like the above with a high straddle (and substantially less than 90 degrees between the two wires below the yoke. However because the Blackburn rack attaches only to the inside of the stays the yoke was set low to avoid the wires fouling the rack, with resulting angle a little greater than 90 degrees. So one of the brakes presumably has greater mechanical advantage......If the shimano instruction is right it'd be the front.
So are the Shimano instruction right for the strongest braking ?........
if the arms are horizontal (i.e. cable attachments level with the bosses) the straddle height makes no difference. With boss spacings as you describe, I'd expect the arms to be close to horizontal.
With the same brakes on wide-spaced bosses, the arms can be set more like a mid-arm canti, and here low straddles make for higher brake MA.
If using PTFE tape I recommend applying it to dry bosses, with a smear of grease inside the arm bushing.