I might just be imagining a difference but I've done A/B comparisons between the USB stick and the CD on various favourite albums (Moondance, Songs In The Key of Life, The Trinity Sessions etc.) and the CD just sounds a tad fuller.
Whether there's a difference in how my Denon AVR4500 processes the binary code received from the USB music is doubtful, but on checking just now I was inclined to turn the volume down one db on that input at my usual wife-friendly volume (-16db) to prevent the music from travelling, probably solely down to confirmation bias of course.
However, there's also the fact that navigation via remote is easier using my Sony 4K player, and that - for me at least - even the small effort of putting in a physical CD just seems to make it more of an event to be enjoyed and cherished.