The reason PDF/X-4 settings are installed in that location is a feature. Beginning several CS versions back (CS2? can't remember) in order make sure that all applications of the Adobe Creative Suite which creating PDF files (InDesign, Illustrator, Photoshop, Acrobat Distiller) were consistent, they began sharing common settings files.
In InDesign, Illustrator and Photoshop, they're called PDF presets. In Acrobat, they're traditionally called setting files. They are stored in a common location, which is the path referred to. They also share another folder where customized PDF presets can be stored.
The PDF/X-4 standard supports features like transparency which Distiller can't work with. So within the Distiller application, its name is "cloaked" so it can be inadvertantly selected. As to why they still show that message on startup, I have no idea. That should be cloaked as well.
However, PDF/X-4 would be the appropriate setting for newer RIPs which support live transparency like modern Adobe PDF Print Engine RIPs. These RIPs are not using PostScript files but can consume native PDF files. But this setting isn't appropriate for Distiller which is built around PostScript.
