Please confirm this is Roon core/server running on both?
If so its possible different versions of Roon are running on each. If so, tehn its very possible the resulting sound could be somewhat different.
Even if same version running on exactly same OS on both, then next thing would be to make sure all Roon setting that affect sound quality (everything short of any added user defined DSP) are the same, for example volume limiting and any other parms that may affect the streaming. I know there are many that may be somewhat different with version but can’t list them all off the top of my head.
Of course an easy first check to compare is to examine the streaming pipeline in play using the Roon endpoint. Is the processing exactly the same in both cases being compared? If not that alone could very well result in a difference in sound.
Assuming streamer is similarly isolated from any network noise (from server of any other devices attached to the same network) as you indicate, and assuming you are using Roon to stream in both cases, changing only Roon server/core hardware my bet would be differences in teh Roon software implementation on each is most likely to result in significantly different sound.
Doesn’t Roon have their own optimized version of Linux (Roon OS) optimized for Roon? Do both servers use that? That would seem to be the best choice of OS to run Roon core/server on.
I run Roon core/server on WIndows. Not optimal, but still works pretty well and sounds very good. I might move to an appliance with Roon OS someday just for kicks. I removed a lot of unneeded programs on my Windows PC and turned off a lot of resource hogging features to help make Roon happy running there. My only issue is periodic slowness with the GUI. All my Roon devices connect over very strong Wifi.
Mysteries.....cheers!