Hey! I too have a mix of audio players for my Mac Mini. Audirvana, Pure Music and Media Center. I have been using Media Center almost exclusively over the past month. To play a mix of Redbook, Hi Res, and DSD files.
To answer you question, the answer is no you do not need to create a separate instance of your music files. Probably one thing I do different than you, is I do not not let iTunes organize my Music library, which is just personal choice. Regardless, I can load Audirvana with iTunes and use all the same music files from the same disk, as when I launch Media Center. Any library information that is used by Media Center is kept in a separate folder(s) than that used by iTunes, so it will not mess with your files. And unlike Audirvana or Pure Music you do not need to do a special import of either FLAC or DSD files.
Happy to answer other questions you may have as I have the advantage of having had more time to tool around with it.
In fact just today I completed moving all music files to a NAS, and I now point to all my music files on the NAS and and the Mac Mini accesses them via wireless (no ethernet handy for the Mac Mini, just for the NAS).
Cheers.
Barr