file type subfolders: good or evil?

The new method of forcing file subtypes into sub-folders (image, file, media etc.) is, for me, sort of a disaster. It completely torpedoes my ability to integrate v2.0 into an existing web site because the editor imposes itself on the existing file system rather than working with it.

I've solicited feedback from the IT people that manage my CMS product's installations and so far its universally negative. One of the issues is that -- for security reasons -- each content page has its own upload folder, thereby segregating uploaded files in case one editor/user has permissions to see a page and its objects but is restricted from another.

My system uses ColdFusion and so far it looks like I have been able to defeat the system's imposition of a global upload folder, so I can set my own on each editor call, as well as defeat the system's imposition of separate folders for each media type.

However, shouldn't this be built into the product instead of having someone hack it in? Is it off-base to expect the editor to work with the file system it is given rather than have it impose itself on that system and force an artificial structure?

Finally, as a project contributor I recognize the value of this editor. Regardless of whether the above changes or not, if I can get it running and it performs well in beta the project is going to get another paypal donation. Its not like I don't appreciate the tool. It just seems like this one element is a wrong turn that doesn't need to be there.