It's a one-step process that Mazda won awards for, and it's been cursed by 3 owners ever since. Primer, colour and clearcoat layer go on all wet together and separate to their respective layers once on the vehicle. This allows them to use less paint (less overspray as it's all done in one pass) and use way less energy as it only has to get baked once.
What it's seemed to mean to you and I is that some owners have complained the paint is 'more fragile' then their last cars was. Mines held up well for two years now, but some have been peppered with chips. I haven't seen a study comparing the strength, flexibility or thickness of the 3's paint to anothers but anecdotal evidence suggests it's worse all-round.
Flex-wise, I guess it's petty damn good, after seeing photos in a recent "Rear Bumper Damage Question" thread by igor2.
But yeah, there's a clearcoat, though some have opted for a bra anyhow.
vaBooM... the flake is normal. Check out another metallic job on a different manufacturer in a parking lot some time. I guess there's a possibility some of the top-most flakes migrated or stuck up into the clear layer a bit while drying and appear more obvious than others... hard to say. Those flakes are what makes any metallic paint job look metallic though.
