The atmosphere itself is not the problem: I tried deleting the whole folder and reinstalling several times to no avail. Maybe the linkalho app is modifying something inside the AMS folder of your switch 1.
Either way, I am assuming the issue is related to the fake nintendo account linked to a second user. The 2.0.0 version is probably doing some kind of internet connection check when prompted to call a second user. Then, the game verifying the account of the said user is a fake (because of linkalho) is somehow crashing AMS.
Weird, huh?