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The above is correct. You cannot organize them since the application expects them to be there.

But really, there isn't much of a reason to be looking in that folder unless you are troubleshooting.
 
To add a tip to make it easier:

When you are in a folder, type the name of the preference.

For example: com.apple.Finder.

"com.app" will bring you to the right section and you should be able to pick it out easily.
 
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