It's no surprise that vinyl and digital are different. Different mastering techniques, playback equipment, recording chain (often), bandwidth, dynamics.
So it should be no surprise that a system optimized for one, doesn't sound as good playing back the other. Music Room One, for example, has been optimized for digital audio reproduction. Michael Fremer's listening room has a vinyl focus. The results for each are predictable. Vinyl optimized systems sound best with vinyl, and the opposite tends to be true for digital.
I have yet to hear a room and system that performs with equal sonic splendor for both playback mediums. Perhaps they exist. I have not heard every room, though over the last forty-five years I've heard a fair number of the best.
In my opinion, it's best to focus setup and equipment choices on one playback medium or the other. Trying to get both perfected is likely going to end in mediocrity.
Some thoughts on the subject might be helpful. First, it's important to recognize each medium's strengths and weakness, then focus on those highlights. For example, the toughest challenge in a vinyl based system is getting the music extracted from the disc: focus your money on the table, arm, and cartridge. The greatest difficulty in a digital system is converting the bits into analog: focus your money on the DAC.
Better to have one type of playback be world class, than both mediocre.