Very interesting Sylvester. Can I summarize your point as something like the following?
1. There are some passages in the suttas that seem to be very difficult to interpret.
2. Some scholars, such as Ven Nanananda, have reasoned out particular interpretations and they feel that the Theravada have erred on some key points.
3. Other scholars, while agreeing that the Commentators missed the point, would argue that the key problem is actually not understanding the Upanishadic background. When that is factored in, they become much simpler. As Sylvester explains, if you take Upanishadic references (e.g. the "All" not being the Buddha's usual "All", as Ven Thanissaro assumes, but the Upanishadic "Ground of Existence") then much of MN1 looks less mysterious.
It is fortunate that we have access to various perspectives.