I agree it is usually the length from the centre of one clamp to the centre of the other, i.e. 'hypotenuse' (although it isn't really a right-angled triangle because the steerer tube isn't vertical). This means that (with the same length stem) the forward reach reduces as the angle increases, in much the same way as it would with an angle-adjustable stem.
Retailers don't always know what the correct measurement method is, e.g. see contradictory Q&A answers here;http://www.wiggle.co.uk/bbb-bhs-25-highrise-oversize-stem/
You may find this page usefulhttp://habcycles.com/fitting.html