You make it sound as if Sapphire had to hire an army of hackers to reverse engineer Apple's EFI ROM deep in the bowls of Sapphire's state of the art Apple Mac Pro Research and Development complex. More likely it's 2 or 3 underpaid software dudes in some basement writing the ROM while in constant communication with Apple engineers. Most of the cost will be in the limited runs of Mac specific coolers, backplates, and ports.
Sapphire charges a premium for this card because they can. It's that simple.
The ports are standard fare even on the PC side, so that part of your argument's shot. And Apple's EFI is their own version, based on EFI 2.0. It gets worse if you have a 1,1/2,1 Mac Pro which is the 1.0 spec before it became standard. There's a reason one BIOS is for Windows 7
UEFI and the other is an
EBC, and it isn't for kicks and giggles.
The drivers are in-house from Apple. Vendors don't do driver updates for OS X on the graphics front. AMD certainly doesn't, at least not on their own - they work with Apple's software engineers, with the Apple folks doing the brunt of the heavy lifting.
Contrast this with the days of the HD3870 Mac Edition, where AMD made the drivers (and one last version of the ATI Displays software for OS X before it was all handed over to Apple). The 3870 Mac Edition was a Sapphire designed card BTW. Originally they were going to use an HiS board design, but it didn't pan out, so they went with Sapphire's design instead. I still have my 3870 here from before I got my 5770, and then a 5870 (giving the 5770 to a family member for their PC).
As for the cooler, the design is a stock design, and only the artwork/coloring is different. That's a minimal cost right there, and the backplates cost pennies as well. Given that the Mac Pro's PCIe Bay Fan blows directly onto the card, there wasn't a whole lot of engineering work that had to be done to maintain proper cooling. It's essentially the 5870's heatsink design.