Some systems (e.g., Debian, and derived Linux distros) make an exceptional effort
not to randomly change user or system settings (via debconf, and governed by Policy).
This has some limits -- it largely applies to systemwide, not user settings, user dotfiles are generally outside of scope (though are also typically unmolested), and some packages, including Firefox, manage to introduce their own configuration management schemas and misbehaviours.
But yes, the general idea that software updates do treat user and local configuration as sacrosanct is well-established, decades-old practice, in at least some parts. And goes a long way to establishing and sustaining user trust in those systems and their update processes.
Mozilla face numerous challenges, including a large multiplatform largely non-expert userbase operating in an overtly hostile environment. The whole browser extension regime is a very unsatisfactory compromise itself. There remain lessons which might be applied from Debian.