The 3DS rom is a 1:1 backup of the NAND contained in a cartridge. It was not edited in any way. In a way, the Sky3DS just imitate the nand of a real cartridge. The difference is that you can change what is on that NAND, a thing that, obviously, is not possible with a real game.
The removal/insert process is just the time during the switch. The Sky memory go blank, the Sky loads up another game and copy it to its nand/memory, the system acts as the user just change a cartridge.
The main part of the Sky3DS thing is the hardware and how does it work to change the game in detail. Things that we wrote are just simple observations. There is work to find how the cartridge really work, how they have to emulate it, which hardware they should use, what they should add to turn a simple "fake cartridge" into a fake cartridge that allows to load every 3DS games.
Not that easy, really.
