You cannot have both latest firmware Atmosphere + SXOS on chipped Mariko.
Upgrading Mariko sysNAND to 12.0.2 and beyond will break SXOS working emuNAND for good.
My son's Switch is a Mariko w/ Sysnand 11.0.0 and the latest Atmosphere + SXOS work fine. The only limitations for Mariko switches are you can never update your sysnand beyond 11.0.1 and you can't use any of the dual boot setups that use the RCM payloads. Updating Atmosphere's emuMMC to the latest firmware version also works just fine.