Within iTunes are settings that you instruct iTunes what to sync. It is merely checking boxes. I do not know what you mean by permissions. Unless by permissions you are referring to the copywriter protections that Apple as well as other sources require. This goes back to the old Napster copywriter protections lawsuits.
That's the DRM (digital rights management) protection which prevent other players playing their content.
Apple has "fair play" DRM system, the iTunes music with .m4p extension, audio book with .m4b extension, and video/movie with .m4v extesion are all DRM wrapped.
Napster and other online stores like Rhapsody, Amazon Unbox, Blockbuster, CinemaNow etc use Windows Media "plays for sure" DRM system, music or movie downloaded there are protected wma or wmv.
Zune Marketplace from Microsoft also provides protected wma and wmv by employing another unique DRM system.
Now you might know why the music you got from iTunes Napster couldn;t play on your Phillips MP3 player
Generally, DRM removal software can help you with it, as they can strip the DRM protection (playback license in fact), convert music or video to various formats that can play on various players.
I know There are professional DRM converters
I have been able to burn music legally acquired which is easily added to iTunes .for example, if I get a free song from Starbucks, when I back my iPhone to iTunes it gets added to iTunes.