Excuse me... what? Where's the Buddhism in any of this, all I see is a strange personal amalgamation of beliefs and almost what seems like contempt towards science and atheism. How is your position any different from presuppositional apologetics without the Bible thumping? You merely assert that the world is rational and so are our senses, how is that in itself rational or even a defendable position when you agree that the matrix scenario is possible, though unlikely in your own opinion? At least you do use the term "I believe" or "we have grounds to believe" rather than stating for a fact.
Atheism is merely a single bit, an on/off position on the question of "do you believe in a deity/deities?" with an answer of NO. Just one god less than a monotheist. It would be easy to argue that any possible deity or combination of deities conjured up by the imaginations of any number of people could be correct. Therefore, quite simply, any other mental constructs and worldviews derived thereof, such as the rationality of the universe, are irrelevant to the very basic question of whether or not you believe. Further philosophical musings around the notion of atheism, or the fact that there are apatheists that simply don't care whether or not there may or may not be a deity or deities, you should probably take up with them instead of dogmatically asserting inherent errors in their worldview without even bothering to understand it on an individual level.
Science relies entirely on the assumption that natural laws are constant and "materialistic" and can not be randomly turned on or off through supernatural means. It also relies on the assumption that whatever can be measured, verified, quantified and repeated reliably has to be inherently true no matter how irrational or unintuitive it may seem. Such as quantum physics and time dilation due relativism where GPS satellites wouldn't work properly if they didn't adjust for it. We can not even begin to understand any of this with our limited senses, without a leap towards the irrational and simply trusting a materialistic externalization of our senses, such as the large hadron collider that relies entirely on previous mathematical and physical findings.
As it is with atheism, science in on itself has nothing what so ever to do with how people might possibly adjust their worldviews based on the evidence represented to them in a scientific (or religious) light, just as theism in on itself has ultimately nothing to do with the particulars of the beliefs, creeds and dogmas one might formulate around the notion of there being a supreme mind, or minds out there that might or might not have created this whole mess in the first place. Even if someone asserts that theism is religion, it doesn't make it so when the very definition of theism is merely a part of what makes up the definition of religion, which requires a collected system of belief, cultural constructs, possibly moral values that are not inherent to theism. Belief, theism, religion, they're all different animals, but you can interbreed them into quite the strange animals. Corruption of science (whatever you mean by that) does nothing to change this and it's just cringe-worthy to read such nonsense. Individual people have ideas and act upon them, not institutions of science or atheism, do you get that? Don't generalize please, would help greatly with representing yourself in a more positive light unless you're just speaking out your mind without any intention of persuading anyone.
Science and philosophy are two separate issues and people should understand this. Philosophy is NOT logic, but it utilizes logic in the search for wisdom. Just as skepticism and rationalism are fundamental to philosophy, so they are to science. Science is merely the extension of philosophy into the study of the physical instead of the methaphysical using the same framework, while philosophy can also extend into an ethical and moral framework and arts. They're not exclusive, however, falsifiability is the very fundamental basis of science, while philosophy doesn't require it, just like your assertions.
Where is the rationality in relying on conflicting personal accounts in the way of measuring or quantifying the supernatural aside from using argumentum ad populum fallacies?