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The sitecustomize.py file is totally available, and the only limitation there is packages can't inject themselves into it on installation. And if you want to trigger it on a package import then you totally can (though there's *another* discussion about that being a bad idea).
.pth files really only satisfy the "run at startup because I'm a dependency of something that my user wants and don't make them opt-in to my changed behaviour", which I don't like :)
If encodings need to be available without an explicit import, sure, we can add a point for those. Import hooks can always be injected by a package __init__.py before the importer will try and resolve the module, so nothing is needed there. But having a PEP with specific use cases to argue about is the way to create new mechanisms here. I don't agree we need a solution before declaring that the old way should be avoided and will eventually be removed, provided we don't add noisy warnings until there's an alternative.