Marc,
I believe Wim's question is slightly different. He is aware of the custom styles feature, because he used it to manage the widths of different sections in the blog before I provided customizable widths. But it is good that you explained the feature out here, given that I am a lazy jackass when it comes to documentation.
Wim's original question was more along the lines not going beyond the Suffusion folder, but storing the custom files (particularly images) under the theme folder itself. I know you could create a folder outside the theme folder, somewhere in the root, which will let you be upgrade-proof. But what if there was another way to do this from within the theme itself? As you stated, you are using a workaround by keeping yourself safe from the complete overwriting. But something leads me to believe that a complete overwrite doesn't have to happen when you do a theme upgrade.
Case in point: it doesn't happen in Atahualpa or Thesis (BTW Marc, if you think my options are good you should see Atahualpa. That is the Numero Uno when it comes to options). It is kind of frustrating to not know the answer here. In my initial design I had suggested the use of a a file called custom.css that you could put your styles into, the same way as you do in the "Custom Styles" option. Then I found out that it was getting overwritten. That is how this particular option came about. I was loath to suggest that the user create a custom folder/file outside the theme and set permissions for it, because it seemed very unprofessional, for the lack of a better word.
