Assumption 1 reads a little differently than your explanation of it. That is to say, your assumption first asserts the rational nature of the universe, and your explanation asserts a seemingly limitless capacity for science to apprehend the physical nature of the same.
"ALL" implies exhaustive knowledge, but science admits that potential cannot be reached. Science does not yet have an exhaustive explanation for gravity, though it is unseen. It's effects have been well-quantified (though not completely throughout the universe), and its effects are seen continually, but science hasn't completely exhausted what can be known about it. Do you think science will ever know what is the "ultimate cause" of gravity?
Science does not typically think so highly of itself, but it must act as if one day it will find out. That is most like what you are trying to say. But does science have the intellectual capacity to determine the ultimate cause of gravity? What if it is, objectively, the God of Abraham, Isaac, and Jacob? Would science cease to be science if it should arrive at such a conclusion?
At the same time, by admitting to limitations it does not necessarily follow that a quest for knowledge is either bound to be fruitless or "pointless." Science takes place because man is curious by nature. He will explore the universe with or without an end in sight. But, as you said, the only reason man is able to excercise his curiosity is because the universe is "ultimately rational," not unlike an intelligent designer.
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I don't mean to imply that the ability of science to find explanations is in fact limitless. Rather, the basic assumption of science is and must be that it is possible, at least in principle, to find an explanation for all phenomena. Like any other assumption, this may or may not prove to be true.