Usually the machine shop will measure the diameter of the piston at a point exactly .500" above the bottom point of the skirt. Then along with the piston manufacturer's recommended piston to cylinder clearances, they can determine where to set the final hone.
The different piston manufacturer's clearancing can vary slightly, but they are all tested for their expansion/contraction properties at 72°F. It's an industry standard. There are two common types of aftermarket piston materials used that I am aware of....4032 and 2618. 4032 is called high silicon aluminum alloy. 2618 is also an aluminum alloy but it usually contains very little or no silicon. The 4032's are used in fairly mild apps, where the 2618's are used in more radical setups that don't see much street use.
The silicon in the 4032's helps to minimize the expansion/contraction so the recommended piston to cylinder clearances are usually a little tighter than the 2618's with no silicon. For instance, JE recommends a .0025"-.0035" (25 to 35 ten thousandths) minimum clearance with their particular 4032's. Then if you have a power adder setup, you will usually want to factor in an additional .001-.003".
You have also make sure that the particular piston you choose will have proper valve clearance, rod clearance, and the one some overlook...crankshaft counterweight clearance.