You could do a symlink, on most systems that wouldn't be a problem. You should always backup any files before overwriting them like that though, just in case something doesn't turn out, you can always revert back to the working version.
The historical difference between the 2 files is actually pretty obvious, even though it's not a standard followed practice, the XF86Config-4 file is used when you are working with XFree86 of version 4.x, and the XF86Config is for previous versions. But, as I mentioned, this is not always the case, and doesn't seem to be as common a practice as one would think.
Cool
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