I use proton pass and have the same issues as the author. Whenever macos/ios is in the mood it lets me use it to store passkeys, else it is an endless maze of bugs and confusion. Proton pass supports passkeys but the OS does not always let it communicate with the website.
Any chance that this is actually due to websites requesting weird WebAuthN credential parameters (e.g. enforcing attestation, which software implementations by definition will not be able to support) or using the legacy U2F API? In my experience that's usually the culprit.
No idea. I do not have the technical knowledge neither the time to check sth like that. I am totally clueless even as to where and how exactly passkeys are stored in my computer. For me they just work until they don’t. It does not really help in trusting them as password replacement.