Can't you suggest it to them via their Github and see if they say "OK" to the idea?It would be nice if Atmosphere added an update folder where anything in it would replace the existing Atmosphere files at boot. Or have some sort of API where it will replace certain CFW files then force a reboot like how Nintendo does it with OFW. The way it is now is annoying because it means you can't update CFW if the only device you have with you is your Switch. Also makes it harder for people new to CFW to update. I still think a major reason SXOS was so popular was because unzipping Atmosphere files to the correct place is genuinely difficult for people who aren't balls deep in to this stuff like we are. It's amazing how incompetent the average person is with technology considering how we're surrounded by every second of our lives. If people were as good with tech as GBATemp users and scene devs like to believe Apple's Genius bar and Walmart's Geek Squad would be out of business.
EDIT: Honestly, if it was possible to just add the zip file and it would update. It would save so many headaches for newbies.