When it comes to you thinking that it's "a big problem" that applications that are installed will place files on the root partition, I can only repeat that you are wrong. Again, this is, typically, how Linux systems work. Installed applications have specific places where they should be placed to be in tune with the rest. There has gone a lot of time and effort into planning the best way to separate applications, data and configurations in Linux systems and Debian is a pretty good example of this.