If a number system has a transcendental number as its base, would these numbers still be called transcendental in that number system?
For instance, the standard statement that pi us transcendental would become the pi is transcendental in Q (the rational numbers). However, pi is trivially not transcendental over Q(pi), which is the smallest field possible after adding pi to the rational numbers. A more interesting question is if e is transcendental over Q(pi); as far as I am aware that is still an open problem.
(I'm not sure what "the elements of the base need to be enumerable" means—usually, as above, one speaks of a single base; while mixed-radix systems exist, the usual definition still has only one base per position, and only countably many positions. But the proof of countability of transcendental numbers is easy, since each is a root of a polynomial over $\mathbb Q$, there are only countably many such polynomials, and every polynomial has only finitely many roots.)
Proof of what? Needed for what?
The elements of the number system are the base raised to non-negative integer powers, which of course is an enumerable set.
> transcendental numbers are not enumerable
Category mistake ... sets can be enumerable or not; numbers are not the sort of thing that can be enumerable or not. (The set of transcendental numbers is of course not enumerable [per Georg Cantor], but that doesn't seem to be what you're talking about.)