On actually looking at the initial changes in the PR:

* declarations that aren't part of the stable ABI in any version (i.e. "#ifndef PY_LIMITED_API", "#if !defined(PY_LIMITED_API)") should move to the new directory

* declarations that are part of the stable ABI in *some* version should remain where they are (i.e. in "Include/*.h")

In your initial PR, the only API that subtle distinction affects is PyObject_Calloc (since that's a new addition to the stable ABI in 3.5+), and moving that back to the public header means you can add the desired "Py_LIMITED_API is not defined" check to the header in the new directory.