I don't have/need a sub, so I have never noticed the "phase" issue. Really liked this album for a long time. 10/10 from me..
I believe you would have the phase issue regardless if you had a subwoofer in the system or not. With no sub, the LFE channel would just be folded into the L/R mains. If the LFE signal is out of phase it will cancel bass information when it combines with similar bass information from the main L/R channels. Same with the center channel. Out of phase bass can cancel whether it is combined electronically or acoustically.