I wouldn't say that there is a tolerance issue. Your Eneloops seem to be a wider battery than standard AA batteries. I had a customer send me some, and I had tried them in an early version of our light awhile ago. They worked no problem. That light, is not the same as the current light. If we had a tolerance issue, the AA batteries wouldn't fit. There might be a tolerance issue with the Eneloops that were built.
The shorty can definetely hold it's own against bigger lights, but as you pointed out, burn time is much greater on a can light.....followed by price tag, size, and bulk. The Shorty has a place in the tier, some prefer it and some don't. If you want to factor burn time into the discussion, then you should also factor in size, easily replaceable batteries, easy to find batteries, and 1/15th the price of the popular can lights
I wouldn't, however, throw build quality out on this light. The light is actually built with EXCELLENT quality, and holds it's own against lights 15x as expensive...as long as you are OK with putting in new batteries after every dive or two depending on useage.