When you have total kernel control, you can do anything you want on the device, including modifying its firmware to work the way you want it to work. It is not that hard as you think it is. The problem was and still is to get an exploit to get you kernel access in the first place, the next steps are a piece of cake for a team of talented programmers... Does the PSP have a problem loading roms instead of UMDs? Does it have a problem running custom code? Did the games need patching of any kind? Well, maybe in the beginning, but as hackers became more capable and more accustomed to it, they modyfied it to play everything untouched...
So either the Gateway made their solution in this way to profit, or their hack is not giving them total kernel control and just allows them to use a fake 3DS cart.
I know it is difficult to create a cfw for the 3DS, but that is where all the fun is, and the scene will be better for it in the long term.