I'm not really familiar with these objections to the Burmese vipassanā approaches, but AFAIK Burmese vipassanā doesn't necessarily require adherence to the commentarial two truth paññatti vs. paramattha distinction. Ñāṇananda practices and teaches vipassanā meditation which he learned from Ven. Ñāṇārāma, who was himself trained by Burmese monks in the Burmese vipassanā method. So it seems to me that these are two separate issues.
That's good to know. Much of "Seeing through" reads as if it came from Mahasi: "seeing, seeing...".
My reading of Ven Nanananda's discussions of bhavana is that he does seem to advocate beginning by "breaking experience down into simpler bits", just as in approaches I am familiar with. However, he objects to taking those "simpler bits" to be "ultimate".
And this is the crux of the issue: Those "simpler bits" are also conventional and not ultimate things in any way, shape, or form. The entire path uses conventional designations from start to finish, and it's misguided to assume that those conventions represent a real substratum of experience (i.e. an "ultimate reality") independent of those conceptual categories themselves. The culmination of cognitive liberation occurs when those categories are also transcended during supramundane meditation.
And, as Tilt says, I don't think it is necessary to designate such things as "real". The Path is, after all, just a raft...
On the other hand, I do feel that too much can be made of the "problem" of believing that there is an "ultimate reality in there somewhere". Unless a practitioner is extremely
naive and/or poorly instructed, it is quite obvious that one progresses through a series of "peeling away layers of delusion". [Oversimplified] One see that a "leg moving" is a complex combination of sensations, motions, and thoughts, and feels proud that one is "discerning khandhas and elements". Then, after a while, it becomes obvious that this "reality" is just another layer of concepts... [/Oversimplified].
I've no idea how it ends, but it seems to me that the important thing is to keep examining, not the motive for examining.