The goals of Commander are to avoid having unnecessary packages, features and donations perks being enabled or bundled by default. That way, the user (aka, the developer), who is planning to use it, won’t really have to spend a lot of time, checking every command/feature one by one to determine whether are they actually beneficial to moderation, or at least their own game. And Commander does that by simply not bundling anything that has nothing to do with moderation.
In which, in other administration systems (excl. cmdr), does contain quite a lot of unnecessary, abusive, game-breaking, and irrelevant features/commands when you installed it.
Considering a lot of users do not really know how to code at all (coming from my experience with Commander, witnessed a lot of people happened to struggle in installing Commander, even if it is really easy with tutorial provided). I can tell that majority of people do not bother messing with the system, so they can get rid of those useless features/commands.
Lastly, we never said those administration systems that you’ve provided are crappy, so /shrug.