You might get away with .0045" on a street bike, but I wouldn't recommend it. Steve Maney and I both sell the same Norton pistons, made by JE to our spec, and we recommend and use .005" clearance. Guaranteed to seize immediately if you use .002" or .0025". That's what JE typically recommends for their forged pistons in Japanese bikes, and that's what they size their pistons for in a standard bore size. The instruction sheet that comes from JE with the pistons calls for .002" or .003" (depends on bore size), and that might be what the machine shop is reading. I cross it out and change it to .005" on the sets I sell. If you have their pistons made for a standard Norton bore size, you will need to hone the bores out another .003" or so for proper clearance. On special order, you can have them make pistons sized for .005" clearance in standard bores, but you have to specifically ask for it.
Jim Schmidt just went through the process of sorting all this out for his lightweight rod/piston sets, so he might have something to add here, if he's watching this thread.
Ken