There are a lot of people complaining about having to use the authenticator app to use security keys for their Proton accounts.
The reason why that was the case was because all Proton apps didn’t support security keys, but that’s changing:
https://www.reddit.com/r/ProtonPass/comments/1eyix18/securely_log_into_proton_pass_on_mobile_using/
The moment they will roll out security key support for all the apps, they will probably remove the authenticator app requirement.
Looking back, I now think its a good implementation for when you lose all your security keys for some reason.
But I was with your sentiment when I first enrolled my Yubikey, thinking this isnt a very smart implementation.
I have tested this with all the Android apps, and all except the Wallet app already support this. However, neither Pass nor VPN will work if you have installed the F-Droid version, which I hope Proton will implement soon.
You have always been able to simply add a TOTP code to your yubikey for proton