4.6 pistons usually have a deck clearance (top of the piston to top of the block) of .008. The 5.4 engines have a substantially larger .120 deck clearance.
The three valve pistons have an exhaust relief cut on both sides of the piston so that the piston can be used in either bank to accomidate the variable cam timing. The reliefs are on the edge of the piston, not in the dish area. Most 2V and 4V pistons do not have reliefs (dome pistons are a different story) and they would be in an entirely different location if they did.
I would not use a 2V or 4V piston in a 3V unless you want to possibly bend an exhaust valve.
Get an aftermarket forged 3V piston (Manley, Diamond, Probe, Mahle), they have all the compression ratio combinations you would need for most applications with the proper reliefs.