Well apt has tools that help you install it through dpkg and manage it through apt, just not many use it.
What I am wondering is how they solve the dependency problem, like say something depends on bash and you remove bash with rm do you get any warnings or help or just a broken system? (This is more for when it is part of gobo and not installed from source).
Removing bash using rm would probably be a bad idea.
Although I think using the filesystem for this purpose is a good idea -- you get parallel-installed versions for free, and it's more reliable and transparent than what you get from rpm -- you're right that just deleting stuff willy nilly won't work. You still need to manage dependencies, and dependency graphs are not easy for humans to keep in our heads.
What I am wondering is how they solve the dependency problem, like say something depends on bash and you remove bash with rm do you get any warnings or help or just a broken system? (This is more for when it is part of gobo and not installed from source).