If you look carefully at the HOWTO on annotations, you will find that there is no designated type for naturals. Indeed, one can just use the type Int, whenever a natural number is required. If we introduced a special type for naturals, that would cause a lot of confusion for the type checker. What would be the type of the literal 42? That depends on, whether you extend Naturals or Integers. And if you extend Naturals and later somebody else extends your module and also Integers, should be the type of 42 be an integer?

Apalache still allows you to extend Naturals. However, it will treat all number-like literals as integers. This is consistent with the view that the naturals are a subset of the integers, and the integers are a subset of the reals. Classically, one would not define subtraction for naturals. However, the module Naturals defines binary minus, which can easily drive a variable outside of Nat. For instance, see the following example:

----------------------------- MODULE NatCounter ------------------------
EXTENDS Naturals

    \* @type: Int;

Init == x = 3

\* a natural counter can go below zero, and this is expected behavior
Next == x' = x - 1

Inv == x >= 0

Given that you will need the value Int for a type annotation, it probably does not make a lot of sense to extend Naturals in your own specifications, as you will have to extend Integers for the type annotation too.