My guess would be that the engineer that designed this joint configuration needed the minimum weld shown on the drawing, if you put more weld than is required you've give him more than he's asked for.
Example drawing calls for 1/4 fillet (BS) staggered 3" every 12"
You give him 5/16" fillet (BS) staggered 4" every 12" (he's getting more than he paid for) it'll only cost you more to do more than is required. I'm not sure it would be a cause for rejection, unless you go way overboard(too much heat input, etc...)
My opinion would be to give him "atleast" what the drawing calls for,
John Wright
ps. It's not a tolerance but rather a min. required.