I had the same problem when remodeling my kitchen just a year ago. Well not the direct vent WH problem. But my plumber had a shut off @ the Tee & also at the appliance, even thou I had a gas cooktop & wall oven config. He also stated the same code "excessive shut off", but we installed it behind the appliance that would never be accessed. The shut off at the tee should be fine (i'm assuming that the distance between the 2 is not that great).
As for piping what are you using: Flex or Cast Iron. Cast Iron would be better.
I looked really quick in the International Fuel & Gas Code 2003 & could not find any min. separations but I would play cautious when running any Fuel piping near a heat source (cast Iron & max distance from vent).