One of the annoyances of Linux is working out where configuration information is, following through multiple layers of indirection and files over-riding other files. This looks like adding another layer, another place to look, and if you're reading the man file for a shell (for example) it probably won't even mention that this could invalidate the information contained in that in the man file.
No, it doesn't. The point of modetc is precisely keep both myself and the programs happy: the files are actually stored where I like to keep them, but they can be accessed as if they were stored where the developer intended.