Short answer: It's hard to reprogram them.
Longer answer:
These flashlight have a small computer, or microcontroller on them. This controls the modes and stuff. To reprogram them, the light will have to be disassembled to the point where the microcontroller can be reached. Next, assuming the microcontroller can be reprogrammed, a special tool (or solder a bunch of flywires and clips) must be placed on the microcontroller and a new program must be written and downloaded to it. That's generally how to go about reprogramming a light.
The hard part is getting to the microcontroller and having it communicate correctly with the computer. Some of them have locked memory, some might not be programmable after they are installed (I have no idea, haven't worked on commercial µc before, and only dabbled in it as a hobby), some might be epoxied in and very hard to access.
For the custom mode lights, the microcontroller is programmed with a special tool before the driver is installed, before there is any epoxy, disassembly, etc.
Like I mentioned, I don't work in this field, so take what I say with a grain (or lump) of salt.