Once again you have made some excellent observations.
"I am greatly puzzled by what Wilber refers to as a strict monological gaze of the "eye of the flesh" in regards to science."
Yes, correctly speaking - or as I would say - when understood dynamically -there is no such thing as a strict monological gaze.
Not alone does even the most elementary scientific perception require the contribution of "the eye of mind" but it equally requires the contribution of the "eye of contemplation".
However reduced understanding results from collapsing the dynamic nature of the full experience (involving the three eyes) to a translation that is solely in terms of just one eye. So when Ken Wilber refers to "narrow" empirical science as the strict monological gaze of the "eye of flesh" he is thereby giving a reduced interpretation of its nature (for he is translating a dynamic experience that requires all three eyes in terms of a static explanation requiring just one).
There is a great deal of confusion eveident in terms of Ken's view of science and its relationship to spiritual experience.
In fact he has outlined at least three different positions in his most recent works.
Thus for example in Sex Ecology and Spirit we have the following quote (in the context of an unnecessary personal attack on Fred Alan Wolf) P. 716.
"A true humanist psychology is built upon processes of intersubjective understanding and mutual recognition, about which quantum mechanics has not a single thing to say, not even vaguely, not even remotely, but by all means, let us base our new humanism on this power-driven monologue with rocks".
Of course quantum mechanics does not operate at the macro level of objects such as "rocks" in any case but let us concentrate here on the fact that Ken is defining quantum mechanics in absolute monologic terms.
However in earlier part of "Marriage of Sense and Soul" an important though subtle shift in position is evident.
Thus in the context of speaking about "new paradigms in science" where he specifically includes quantum mechanics he states on P. 39.
"But they are all without exception monological to the core. And thus, as important as they are in their own right, they have little to offer us in terms of actually integrating monological with dialogical and translogical - that is integrating science and spirituality."
So we have now switched from a position where quantum mechanics has absolutely nothing to say (in terms of integrating science with spirituality) to a position where though it has "little to offer" clearly it has something - however small - to contribute. Unfortunately Ken does not clarify what he means in this context and in any case it is inconsistent with the viewpoint that quantum mechanics is monological to the core.
However when we get towards the end of "Marriage and Sense and Soul" a further - and rather dramatic - shift in position takes place. This is a relevant quote from P. 196
"For objective empirical science is no longer relegated to the bottom rung of the hierarchy (which the traditional approach gave it and which contemporary epistological pluralislism still gives it); rather, empirical science is accessing the exterior modes of all the higher levels as well. This moves empirical science off the bottom level of the Great Chain and places it on the exterior side of each level of the Great chain. You can see this in Figure 5-1). Thus objective empirical science does not give us the whole story, but neither does it have nothing to say about the higher domains, which is the untenable stance of both traditional epistemological pluralism (and the crushing error that contributed to the collapse of the Great Chain of Being)."
So in Ken's terms quantum mechanics is an objective empirical science. So we have moved quickly through three positions
a Wilber 1 where it has absolutely nothing to say about the "higher" spiritual levels
to a Wilber 2 where it has perhaps something to say (but which is not specified and in any case inconsistent with the core supposition)
to a Wilber 3 (where though "it does not give us the whole story") clearly can tell a great deal.
In fact the only position that has not been articulated here is a Wilber 4 (where for example quantum mechanics could tell us everything about the "higher" levels).
Surely I cannot be the only person who sees the considerable inconsistency of all this! And remember we are talking about an issue that is clearly central to the integration of science and religion.
The key problem is in fact very simple. If one looks at the subtitle of "Marriage of Sense and Soul" it is subtitled "the integration of science and religion".
However when one examines carefully what Ken has to say it becomes apparent that he is not really dealing with how these can be integrated but rather how they can be properly differentiated in experience. And at this level of discourse Ken does a fine job.
So the subtitle of the book should be more properly entitled "the differentiation of science and religion".
When Ken eventually does get around to talking about integration (late in the book) he only does so in a very general and somewhat vague fashion (which creates major inconsistency interms of his former positions).
For example let me take another quote from P. 196
"For the higher levels themselves are not above the natural or empirical or objective, they are within the natural, empirical and objective. Not on top of but alonside of. Spirit does not physically rise above nature (or the Right-Hand world) spirit is the interior of nature, the within of the Kosmos. We do not look up, we look within."
Just take the last sentence "We do not look up, we look within".
One can rightly counter that the very thrust of Ken's approach to holarchical development is to look up (i.e. the ascent). Though Ken is providing here what in fact is the immanent position on development, his holarchical approach is based entirely on transcendence (i.e. each "higher" level transcends and includes the "lower" stage). Indeed just a few pages later P. 205 Ken comes out once more, strongly in favour of the evolutionary view of development (i.e. the ascent) "because the Great Chain itself is already fully compatible with an evolutionary view".
And of course if the higher levels themselves are not above the natural or empirical or objective, then it is ridiculous to insist that empirical science is necessarily monological. Clearly the "eye of mind" and the "eye of contemplation" are (inherently) within the "eye of flesh".
So the real problem is that Ken employs in rational terms a strict (linear) either/or logic which is only suitable for differentiating experience (e.g. different levels, different quadrants, different eyes).
However for translating the dynamic integration of experience we need the alternative (circular) both/and logic.
Thus when one attempts to move from the task of differentiating reality (at which Ken excels) to the qualitatively different task of integrating (what has already been differentiated) we need to switch logical systems (i.e. move over to the dynamic relative approach which uses a circular logic).
If one continues to try and view integration through the (linear) either/or logic, then inconsistency will abound. And as I have demonstrated it is very easy to find many important examples of this inconsistency in Ken's approach.
There is indeed a means for reconciling these (apparently) conflicting statements made by Ken. However it requires employing - in rational terms - both (circular) both/and as well as (linear) either/or logic.
In other words we require a logic of integration (circular) as well as a logic of differentiation (linear).