Your statement that we will never get to the bottom may be true, but the reasoning is flawed.
Gödel's incompleteness theorems are about mathematical theories, not about physical theories. It may well be that for physical understanding a very limited arithmetic is sufficient. Also, there may be statements that are unprovable, but these might turn out to be irrelevant to sufficiently understanding the universe.
Also, an axiom, by definition, can not be proven. The things that are proven are theorems, statements, etc. An axiom is an assumption.
Eventually, it all depends on what level of understanding you want. But Gödel's theorems have little to do with that.