How can I "reverse engineer" a system of quantum state expressed in complex numbers to its actual natural manifestation (assuming some kind of mechanical tools are developed in the future to do that)?
It's the opposite in fact. Almost everything in the nature works more naturally with with complex numbers. Complex numbers are algebraically closed unlike real numbers as you point out and that is very important part of it. Everything becomes more difficult if you try to force them into real numbers.
Quantum wave function is an explicitly complex object. Making it anything else makes it more difficult.
Here is great and easy to understand explanation: https://www.scottaaronson.com/democritus/lec9.html