I would complain to Linn under the circumstances. If there is a SQ difference, Linn are probably responsible for it. SQ is left up to them in the Roon Ready certification process I believe. Once the bits are handed over by Roon, Linn could be applying some sort of processing to it (not implying anything underhand here) for their own purposes or to achieve the house sound.
Interesting thread here which may be relevant to what could be going on: