From Stdlib Require Import PeanoNat.
About eq. (* Corelib.Init.Logiq.eq *)
Import Nat.
About eq. (* Stdlib.Arith.PeanoNat *)
This prevents writing, e.g. eq_refl in a proof term (except for nat of course).
A possible (heavy but maybe beneficial in the long run) fix would be to change Numbers so that equality is Leibniz everywhere instead.
Or I learn to live with it and stop Importing Nat, but this is painful for a (somewhat basic) course.