I also don't understand how proof checking can be decidable if the axioms are not recursively enumerable. If proof checking is decidable, there must be a way of determining if a use of an axiom refers to a valid axiom. But if you can do that, as long as you can put the syntactic formulas of the system in bijection with the natural numbers (which I presume is the case if this is aimed at computing, and would hope in general that you can write them on paper using a finite string of symbols) you can produce an enumerating program by just running the decision procedure on every syntactic formula and only emitting ones that pass. More succinctly, all recursive sets are recursively enumerable.
But proof checking is still computationally decidable by a provably total higher order procedure. See the following: https://hal.archives-ouvertes.fr/hal-01566393