Been on one Goenka retreat, which I had to leave after five days for health reasons, and read the book. They are an excellent training environment. There are aspects to them which I disagree with, but those are far outweighed by the benefits of the disciplined environment.
does one actually increase mindfulness to the point that they are subjectively experiencing sub-atomic vibrations, etc?
No one actually knows the answer to this, but that doesn't mean it's necessarily harmful. For what it's worth
kalapas (the traditional term which Goenka equates with subatomic vibrations) are not mentioned in the Pali canon, they are a commentarial innovation. However, I am quite comfortable working with post-Gautama innovations to meditation practice. Maybe no one else since the Buddha has been as good, but there's been a lot of time for a lot of people to try a lot of different stuff.
The question to ask when a mythical concept like
kalapas comes up is "What practical issue is this imagery trying to answer?" In this case the practical issue is "What time resolution should I be satisfied with in training my awareness of phenomena?" The answer implied by the
kalapas concept is "All the way to 11, baby!!!"
One could fault Goenka as a scholar for his facile equivalence between
kalapas and subatomic phenomena, but as a meditation teacher, I think he did quite well with it for most of his students, because that kind of thinking inspired a lot of people back in the 70s and 80s. The equivalence is quite dated and stale, now, though, and although it's unlikely, I think the Goenka movement would do well to move beyond it.
Is one penetrating the "unconscious" mind, releasing sankara after sankara by bringing equanimity, etc? Yes, this is part of how it works. Freud's historical notion of the unconscious concerned painful things people repressed because they didn't
want to see them, and the things which got repressed as collateral damage, because they would imply the primary objects of repression. Equanimity gives you the strength to look directly at these things. The book
Disciplines of Attention goes into greater detail about the correspondence between Insight meditation and Freudian psychotherapy.
Do sankaras have physical manifestations when brought to consciousness? Or is that largely myth? I realize there is a pseudo-sciencey ring to it, but how applicable is it to the truth, in your opinion? Depends what you mean by physical. In terms of direct experience of the moment, every movement of the mind corresponds to a physical sensation, in my experience of formal meditation. This is why a technique like body scanning is so useful. Are there sankharas corresponding to specific individual subatomic interactions? No one knows, but I am skeptical. I suspect the answer is "Only if you're observing those interactions via an instrument designed for the purpose." :-)
Or could building mindfulness with anapana sensations result in the dissolution just as well? The last two questions quite possibly show my lack of understanding with the dissolution stage, but having read MCTB among other books, I can't seem to get it straight.
Mindfulness alone is insufficient. You use mindfulness to remember to develop the other factors of awakening (analysis of qualities, persistence, rapture, concentration, equanimity, tranquility), and to remember to view what's arising through the framework of the three characteristics or the four noble truths. Mindfulness is arguably the most critical factor to develop and worth emphasizing at the start, though. You might find that
this essay clarifies things.