If you heard differences when switch hard drive from internal to external even changing brand or model.
It could be various reason.
First, most of the time, it's placebo.
For external enclosure, if you insisted that some **** happened and you heard it, there are several cases that could make it actually happened. Such as;
- Ground (Earth) loops/No ground at all. This problem happened a lot in past but unlikely to happened in desktop these days. However, this **** happened a lot in Macbook/mini system. When it happened, you could heard god knows what noise from your speakers. It could be hum, static noise, motor noise or read head seeking noise. Some stupid audiophile or greedy audio shop would suggest you buy new hard drive that rotate at higher RPM so the motor makes noise at higher frequency and it's more inaudible.
- Introduce devices that has no/bad grounding to your system. It would cause ground loop. If you add devices using 2 prong power cord, you should test it by Volt meter. Disconnect your Raid enclosure USB cable from your desktop keep your desktop and Raid enclosure running and check if there are any differences in voltage between ground of your desktop and raid enclosure. If both are properly ground it should be around zero volt. A few volts "might" be tolerable.
- Your RAID enclosure or some where in your connection are so ****ed up. For an example, poor ventilate cause hard drive to overheat, no vibration damping, using poor quality parts (eg., crystal oscillator, and so on.), or poor manufacturing (got defective one; cold soldering, and such). For USB, contaminate USB power could effect devices connect to its, too. However, these shouldn't happened in nowadays mobo.
- One or more of your device has stray voltage. FYI, in some system, using 2 prong power cord can cause this problem. And stray voltage can be as high as 78 Volts. https://www.youtube.com/watch?v=_7YUaYvcirU
For some enclosures that have poor ventilation, if they're using passive crystal which accuracy degraded when temperature raise, it's likely to have more jitter and "might" make sound slightly warmer and cloudier.
For people who're using NAS, they're unlikely to have this problem because RJ-45 connector has built-in isolate transformer as its specification requires so.
P.S.
I don't heard any **** differences when playing songs from hard drive plug into USB3 dock. However, in my acquaintance MacBook system has similar problem. You should know why by watching video clip, I posted.