No, there are 3 audio outputs offered by the layout of the QNAP chipset. It has nothing to do with your harddrives.
I never tried to use them yet. One of these 3 should be the HDMI output and I think the other 2 are available by the chipset but not wired to any connection. But to be honest: I did not really investigate what internal outputs can be used (and how).
I remember when I upgraded my QNAP, that there was also some kind of mini-Displayport on the board. Some models have also have a dedicated audio mini-jack.
I can’t say for sure, but currently I believe these are the 3 options that are shown in Roon and only available at some models.
Raid5 should not be any issue.
How did you set up your PS Audio Junior + Bridge on the MacMini? The same settings can be used on the QNAP.