I apprecate your posts, Paul, I am not here to disagree or debate. Your experience is your experience and I do not doubt it.
My feeling is that what you describe is a pretty fundamental problem in practice. Reification and attachment to sort of a self, a sense of existence, a vibration, of primordial sound, hell, most of us are attached to far grosser things than that!
Ive also heard similar reports from other former Vajrayana practitioners, one being a former member here, PeterB. Some Zen teachers have told me that in Vajrayana there is a lot of emphasis on energy and power.
Perhaps there are good reasons for this sort of practice though. Perhaps without habituating oneself to a swirling warm pool, it is virually impossible to let it go in a still cool one?
I do not know whether Vajrayana has forgotten about relinquishing each and every abiding and fetter, but they certainly have a lot of teachings to this effect and they hold Nagarajuna in very high regard. As for Zen, which is surely a major tradition within Mahayana.there are many clear instructions to this effect like herehttp://www.spiritual-learning.com/case-27.html
So I am not sure if what you have related here describes the limits of Vajaraya practice, the limits of your lineage, the limits of specifically what you were taught, or indeed your understanding of it. But I do not think this desribes the limits of Mahayana and when you said that it is a hindrance, I think you overstated your case.