Probably for the same reason other systems don't even allow you to run things as root. Warranty, support and liability. If Nokia had simply used the standard debian way, people would have sooner or later get "infected" by arbitrary packages replacing "system" packages. So HAM has some kind of protection for this.
What we also need is fixing the dependencies of many packages. This will prevent breaking stuff with or without --auto-remove (auto-remove should NOT break stuff unless the dependencies are broken).