You are misinterpreting that, so no, it's not an atmosphere issue.
the "lines" you speak of are a concept of set-mitm, which overrides the values applicable from https://switchbrew.org/wiki/System_Settings
and no, the values you speak of should not ever be default, as atmosphere is designed to be used while connected to nintendo, while being able to access eshop, while being able to play online and while being able to pay for games. The usecase where that doesn't happen, and the user profile de-syncs, is in 90% a piracy related problem.
(enable_sync_elicense_request = 0x0 <----- anti-piracy check within NS (the module that does rights management on the switch, specific to digital temporary licenses, gained from nintendo switch online, ex: "free" animal crossing dlc, if one chooses to not buy the dlc, but gains it from NSO, moment NSO runs out, the elicense will revoke itself and the dlc will become deactivated))
