How Klipper works together with user interfaces is detailed here: Klipper Architecture / Ecosystem
Not being a Mainsail expert, I would think that it just calls apt update / apt upgrade to update the Linux OS. If such an operating system update causes issues, it is likely that the issues would have also came up when doing a “manual upgrade” from the shell.
Not sure who is to “blame” here. Definitively not Klipper