Welcome to the LOC! All of us will try to help out.
I'm not an expert on the ML, but will give you a few ideas that come to mind at first blush.
It would be doubtful that it is a torn or "blown" speaker. If that were the case, it would likely sound very distorted, muddy, and fuzzy. That is not what your describing. It could be a crossover filter dedicated to that speaker, or a component in the signal processor. I say signal processor because you talk about that speaker having split second phase delay from all of the other speakers. As I understand it, the Levinson has a "Surround Sound" or what is also called a sound stage feature that is created by some sort of signal processor. If the system is in the Surround mode I would wonder if there might be something going on there that is creating the signal-phase delay. I don't really know for sure. As I said, I'm just spit balling here.
Your Lexus dealer would probably start with changing out the speaker. They will have the OEM Levinson speaker, but at a hefty price. Unfortunately, the dealer is not equipped to diagnose these problems, they only replace whole components. To find someone who can diagnose the specific problem, you'll need to find a qualified car stereo installer. If you want to try the speaker first, ( I believe their 8 ohm which is unusual for car specs.), e-bay or some other supplier will be cheaper than the Lexus dealer. However, because in the ML system all of the speakers and their crossover network are matched, you'll need to be carefull to find a replacement speaker,(if that is what the problem is)that is as exact as possible to the original.
By doing a search of the forums you may find some names of repair shops that work specifically on Mark Levinson.
Others will chime in here who are probably more knowledgeable than I.