Replace AddObject() with AddObjectRef()

[MightyJosip]

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Since Python 3.13 PyModule_AddObject() is soft deprecated. This PR replaces it with newer function, PyModule_AddObjectRef(). It was changed following the way adviced in the official documentation between versions 3.9 <-> 3.14

[Starbuck5]

It's also confusing to see replacements for things that didn't previously have an incref.

[MightyJosip]

It's also confusing to see replacements for things that didn't previously have an incref.

Yea you are right, that comment is mostly for encapsulate_api, and in the current master if I print Py_REFCNT of apiobj, it is 1. However, after this PR it is indeed 2 like you said. I will remove it from those places, and use it only when we actually increase the ref