Here in PA, the Commonwealth of Pennsylvania Department of Labor and Industry feels that construction tolerance is not defined in ANSI A117.1-2003 or in the IBC 2009. Without definition there is no allowance according to PA L&I
Also, construction tolerance is for installation, not design. The design is absolute, and with absolute, water fountains are a protrusion hazard.
The enforcement in PA is to these standards and not the American with Disabilities Act. The feeling is also that commentary is not code.
Also, in unofficial interpretation from the ICC, water fountains should be can propose a protrusion hazard without barriers.
This is not to say, on my part, that common sense should apply, BUT PA L&I is ultimately my boss.