On the Atari, not all users desire having a full unix file system.
I use Linux myself on my PC but I don't see the need for the full
infrastructure on my Ataris. Ataris are Ataris, slick, small and error
free without command shells :)
I see your point, however this is sometimes even not possible at all. Especially for packages like bash or gcc. If you take a closer look at Jo's great VanillaMiNT or AFROS or uMint :) you'll notice that 'clutter' is still there, it just resides in c:\mint\etc, c:\mint\tmp etc... these applications require the Unix filesystem because they are, well, Unix applications.