I'm not sure Amazon doing *one* premium model alongside three value models means they've gone Boutique.
To me it means they don't expect the LTE model to sell enough to get a particularly high volume on the custom modem chip. That quoted price is for a generic (thicker) chip that is produced in very high volumes, not Amazon's custom chip. Which hasn't been FCC-approved yet.
I see the LTE FIRE as akin to the Dodge Viper or Chevy Corvette, a "Halo" product intended for low volumes with low-volume pricing just to show they can play with the "big boys", tech-wise. Think of it as a shot across Apple's bow; "We're closer to you than you like to think."
If you're a value buyer and $499 offends you, that is fine; the product is not meant for you anyway. (You wouldn't be dropping $499 or higher on an iPad anyway.)