Yeah, I think the tire diameters that get plugged in for a "built" bike BB height are a little large. It would be better to list BB height from the axles, but then nobody understands the numbers... "WTF is -0.5" BB Drop?" Negative drop... huh? Anyway...How old is your BS? They may have changed/updated (or measured it with different equipment like a boxxer with a 1.5" non zero stack). The one we had was also around that 13.7 number with a zero stack, etc.
Yes - the BB heights are quite low, but that is why there are 3 of them. It would be a waste to have 3 settings if one of them was too steep/tall for current rider's preferences. And also, the headtube is short enough that you get a lot off range in fork height as well. Pretty easy to raise/lower the front/rear to get the HA and BB combo that you want. Currently mine is in the low position with a BB height around 13.55" or so... for what that is worth.