Yeah, I ran into the same problem when I was trying to get change the location of where files were stored. From what I could tell, Upload Path, Upload Url Path, and Fileupload Url had no effect on any of it.
My motivation for changing the location was because on the server I use, the subfolder blogs.dir/blogid/files/ would be owned solely by Apache, rendering it impossible for users to upload files. What I did to fix this was first modify wp-settings.php, then wp-includes/wpmu-functions.php, and I also added a new rewrite rule in .htaccess (but I don't think this is necessary if you keep the short url of domain.com/blog/files/... ~ blog.domain.com/files/...). While I was at it, I also changed the use of the blogid for user folders, and changed it to the name of their url path (i.e. /blogs.dir/namepath/), which makes it easier for me as admin to easily identify what folder belongs to who.
If you only wanted to change the upload path for a single blog, then the quickest way would be to just add an if statement checking the blog's id and changing the upload location accordingly. A better solution would be to change the code and make it query the database, requesting the upload path for that blog, and if none exists, to use a predefined location. (unless someone has a more viable solution?)