You are correct in that some of the "clean" ammo comes with enlarged flash holes. From what I've seen, this is only so in .45 Auto, and the 9mm, .40 and .357 brass I've seen has typically sized flash holes.
If the ammo is advertised as having non-toxic "clean" priming, there's a good bet that the flash hole is enlarged. (in .45)
Attention Brass rats and other reloaders: I really need .327 Federal Magnum brass, no lot size too small. Tell me what caliber you need and I'll see what I have to swap. PM me and we'll discuss.