If you can somehow ensure the tin foil DOES NOT go anywhere its not supposed to, it will be fine. Some tape can help to ensure this. Otherwise, it may end up causing your Joy-Con to not charge on the Switch or even worse. There is an ultimate list of mods to enter RCM thread here that you can consult for alternative methods.
Because the jig may not always work properly. Not to mention that using the jig alone is not sufficient to load the exploit. It also involves sending a file through the Switch's USB port which is not ideal if say you're out of your house and you turn off your Switch which will involve having to repeat this process. The holy grail method of booting hacks would involve something that isn't tethered or rooted into a hardmod. This may be found in the future so to be safe, it is still recommended not to update. Also, once the CFW Atmosphere is done, we will all be able to update to the latest firmware anyway using EmuNAND.
For a 3.0 switch, it will involve doing a minor hardmod to the Switch such as inserting a paperclip into the right Switch rail then connecting the Switch to either a computer or Android device to send a .bin file to install it. There is an unreleased software-based exploit that you can utilize to install it however we're on the dark on what that exploit exactly is. Presumably, it will be made available the same day Atmosphere is released.