Yes, we are able to derive aspects of phenomena via our measurements but it could be likened to standing on a sea-shore and discovering one or two interesting pebbles while the vast expanse of ocean lay ahead of us, undiscovered. Obviously there is structure to the universe but what I am saying is that what we codify as information is based on our mental predispositions and it is this that is knowable to us. We filter incoming information much as a radio receiver filters different radio frequencies that it is attuned to. It doesn’t mean what we ‘pick out’ as meaningful is a full representation of reality. We are very ‘picky’ in what we choose to call scientific data because it has to conform to something that is going to prove useful to our species. The universe doesn’t care about us so it won’t provide information automatically for our benefit; we have to do this for ourselves.
But, again, axioms based on what? On our natural predispositions which have been formed by natural processes.
The problem here is that you are assuming the universe can be totally described by using mathematics. You can get so far with mathematics but it seems to me quite presumptuous to suggest that something as rigid as mathematics can fully provide an understanding of all aspects of reality. This should not be surprising given that we base mathematic on a relatively few set of rules. What our species has achieved is providing schemas of reality that conform to mathematics but that does not mean most of reality does. We have managed to forge a clear path through a dense jungle of confusing incoming sensations and called it reality but, actually, it is our reality, not necessarily someone else’s. The problem with mathematics is that it is a closed system and, therefore, self-referential so that the only way we can know about stuff is the way it is represented by the formulas we use. In this sense, it is too parsimonious to really* be* reality and again, we are back to relying on something that provides a model and serves us in our cause.