The problem 

It is not entirely clear to me how the philosophy of effective altruism and rationality  addresses what I would call "innate intuition." I feel EA community generally disregard this issue and here I pout my skepticism and hope that colleagues will help clarify this issue. 

(I am mainly referring to Wilson "Consilience" as it seems to reflect the EA philosophy opinion on the subject)

Despite the ambitious aims of EA it becomes apparent upon closer examination that our approach is fundamentally flawed due to its lack of consideration for the inestimable value of inborn intuition and the integral role of metaphysical principles in shaping our understanding of reality.

Our reliance on the scientific method and empirical evidence as the sole means of acquiring knowledge is problematic in its narrow, positivist approach, which ignores the invaluable insights that can be gleaned from our innate intuitive faculties. These intuitive understandings serve as the foundation for all subsequent learning and development, and to ignore them is to deprive ourselves of a crucial source of insight and understanding.

Furthermore, EA's dismissal of metaphysical principles as mere "abstractions" is intellectually irresponsible and represents a gross oversimplification of the complexity and multifaceted nature of reality. Metaphysical principles such as causality, identity, and the laws of non-contradiction are the very foundations upon which our understanding of the world is built, and to ignore them is to undermine the very foundations of knowledge itself.

Finally this approach is particularly problematic, as it ignores the essential role of first principles and intuitive reasoning in guiding our decision-making and moral reasoning. Without a strong foundation of intuitive understanding and metaphysical principles, it becomes difficult to make informed and reasoned choices about how to allocate resources and make ethical decisions.

So I argue that to truly achieve the consilience that he advocates for, it is necessary to adopt a more holistic and inclusive approach that acknowledges the multifaceted nature of human understanding.

Examples

I made an attempt to formulate my thoughts on the subject, but it is very likely difficult to understand without examples, so here are a few.

• Differentiation. I've always thought of things in terms of structures. Something is either connected or not, nothing complicated. In particular I thought of differentiation as an operator of killing structure or increasing entropy. And in some cases we can kill the structure of an object to the point where someone appears by chance. So I looked at the solutions to the heat equation and noticed that the structure increase with time which is sort of strange and does not usually occur in physics equations. So if we reverse time (assuming atoms exist and Newtonian mechanics among them) we kinda get paradox as math allows only finite time before singular points appear. But it is solved when assuming something (atoms) are so uh unstructured that they have random position. This gives correct results. 
• Commutative algebra. I think that main mathematical concepts like structures in analysis or linear algebra-so simple people have same intuition around them. But when it comes to something like abstract algebra e.g. commutative algebra or algebraic topology, lots of brilliant people tend to have fundamentally different intuition around same structures which to me seems immanent
• Galois theory. 

 So what?

Imagine a person who was born blind, deaf, and has never experienced sensory or any other feelings. And yet his brain is perfectly normal. Imagine that person woke up at some point and was able to share information with us. Can we think that his intuition in some advanced fields of science would be useful and sometimes better than ours?

I always thought I had to act rational and pay no attention (or less attention) to my own intuition as rationality suggests. And it is indeed often biased unfair and I can often optimise my own happiness as well as happiness and wellbeing of people around me by acting rational and artistically, based on robust empirical evidence giving me best possible understanding of how the world really works. But now I fell like my own intuition also can be beneficial sometimes (or not). And that's my concern. Can I trust myself? Can I robustly use such simplifications in my head as an examples above or are they  just erasing from lack of understanding? Sometimes I think even full and complete understanding of structures allow some new intuition to appear. And when referring to intuition I mean maybe the color of the surface of topological space you imagine when thinking of Klein Bottle for example. This things can have cumulative effect and result in completely different result in my brain in future, that's why it seems important.