Why is $f_1(x)=x^3+1$ not exactly the same as $f_2(x)=x+1$? $f_1(0)=1=f_2(0),f_1(1)=0=f_2(1)$[...] Then the only irreducible polynomials in $\Bbb F_2[x]$ are $x,x+1,0,1$?
You have discovered that the two polynomial expressions produce identical functions, but the 'correct' definition of equality of polynomial so is 'the ordered list of coefficients match.'
Using polynomials as functions is most useful for identifying irreducibility of polynomials of degree 3 or less. It's true that a nonzero polynomial of degree 3 or less is reducible iff it has a zero as a function. Beyond that, a polynomial with a root is reducible, but the converse may fail. Perhaps that is where you got the idea for this connection.
I.e. Why can't we reduce $x^n=x$?
You can reduce $x^n-x$ over any field. It at least factors into $(x-1)\sum_{i=0}^{n-1} x^i$. Do you mean reduce in some other way?
If you meant that you believed $x$ is irreducible, then continued that "$x=x^n$" and is therefore reducible as well, then you have run into the 'wrong definition for equality' problem again.