Ok sorry for the questions but (in theory) when the CFW is installed why do you need a Jig??
The jig is required to make the exploit work which allows the running of arbitrary code, so even when CFW is installed it still needs the exploit to be run for it to load the CFW (which will most likely run in an emulated NAND rather than being installed to the system NAND). If you were to flash CFW to the system NAND and didn't run the exploit it would simply not load anything.
When you have had CFW on the 3DS it's usually using software based exploits to automatically run the code but in the case of the switch (on latest firmwares) the only exploit is the hardware one so to load into CFW it will need to run that exploit every time it boots the CFW.