- Of course it's a system-wide effect, you're affecting all users on the machine when you write to anything in the Program Files folder.
And if you're the only user? Or all users are allowed equal access to the program? I do see a point of separating things be user on a multi-user computer... not for security, but to have different settings. However, on a single-user computer, I prefer having the entire program kept in a single location so that I can easily find everything. As it is, I have programs that have settings in the program folder, in the My Documents folder (usually in subfolders, but not always), and in the Application Data folder. It's a bit rediculous.