Here is where my ignorance becomes readily apparent...
I have no idea what an MSA study entails, except what I have gleaned here. I don't actually do any of the QS9000 stuff, I have strictly worked in the calibration arena for some 17 odd years.
But...
From what I have learned (possibly mistakenly) an MSA is the study of a measurement system including short-term variation, drift, etc. In this case, the tolerance of the gauge has absolutely no bearing whatsoever. What does have bearing is the absolute error (bias ± the uncertainty of the gauge), its repeatability (short-term), its drift (those yearly calibrations, with data, on a spreadsheet gives a great baseline), the effect of your specific environment extremes on the gauge (I've been in shops with 39°C seasonal temperature swings and they have no idea why they have problems measuring aluminum), and variation between the petite guy that is oh-so-careful and Gunther-who-uses-a-micrometer-like-a-c-clamp.
General rule of thumb in metrology - measurement is measurement, and tolerance is analysis after the measurement process. Tolerance is not a gauge attribute, it is a (sometimes arbitrary) number a design engineer figured his/her gauge should be able to meet (and possibly even meet over time) when compared to the oh-so-elusive absolute "nominal".
So, on a good note, if your gauge variation as a percent looks just like your total process variation, you have a mighty fine process.
In other words - I use tolerance for 3 things. First, it gives me boundaries for computing the recall cycle of a gauge. Second, it allows me to take a gauge's reading as gospel if the tolerance is sufficiently small compared to what I am testing. Third, it tells me when to adjust/repair/replace a gauge, which means my company makes more money and can give me raises.
I don't know Stuart's application, so it is hard to say if % tolerance gives any indication whatsoever. But, if total allowable deviation of a gauge is specified in the quality system as the same as the tolerance, it would be a very good indication of gauge condition and drift.
I hope I wasn't entirely off-base, as I've never needed to look at an MSA manual. I just have to do those uncertainty studies.
Ryan