This type of Debian install doesn't actually replace anything, it just runs in the background. This also means you need to do somethings to be able to access your files from it. I can elaborate on that part more if you decide to give it a try.
To open vi use the following command:
vi
Part of why it works this way is to make it easier to use. By putting the OS in flash you can just insert drives and start using the system without having to go through a firmware install etc. There are also security advantages to doing things this way, the same things stopping you from running custom code stop random malware from running as well.
I agree with you though, I wish by default they (not just Buffalo) made devices easier to customize.