If you are so much bothered by Android design, adjust your POV slightly: consider /system to be recovery partition (you cannot delete anything from any recovery partion of any system, so Android is no exception here) that shares data blocks with main system, created at boot in RAM. Because that it effectively is.

You don't have to resort to ADB to disable these apps for the most part; You can do it in Settings. For some apps you cannot do that in GUI - for Settings itself, for example, so the users don't shoot themselves in the foot. Unfortunately, some manufacturers abuse this and mark as undisable-able apps, that they shouldn't. Over ADB, they can't disable it, so it works for any app, including Settings.