I have the Yellow Sub. from a few years back and have listened to it happily several times (really love this album),
but the box-set one just is more balanced for me, with no ear-bleeding sounds. And that goes for all the albums,
especially the early ones, which bordered on unlistenable for
the high-pitched overtones [unless you were listening on Harbeths or Sennheiser 650 headphones :) ].
The latter albums were much better (Abbey Road, Let it Be, and Let it Be Naked), but still, I much prefer the rounded vocals and overall sound of the box set ones.
Is that Band on the Run a CD or a FLAC file that I need to burn or something? I'm not really up on computer audio.
(But I LOVE my Quad 9L speakers with youtube music. I spend way too much time with them.)