I think you are misunderstanding how the Yubikeys work. Basically it is like having an additional password to your account (don’t worry, I mean this is a safe and secure way).
When you go to setup the Yubikey, you register them with the platform you are using for your account. Any service I’ve seen has allowed multiple keys to be registered. Once they are registered, you can use any of them when accessing your account.
So on your Mac, you’d log in with your master password. Then it’ll prompt you for your 2FA using your Yubikey (Or other FIDO compatible security key). It doesn’t care which key is being used as long as the key has previously been registered with the account.
All of that is to say that no, 1Password shouldn’t be confused when using different keys on different devices. It doesn’t “know” persay which key to use, it just knows which keys it should accept then accepts them indiscriminately.
To that end, if you have multiple security keys, know where each of them are at any given moment. I’d bet that’s why Rose’s spare key is in a locked safe. My spare key is not in a safe, but it is in a locked drawer. (If you do have a backup key, you would also need to register both keys with your services otherwise the backup key won’t work)
I use LastPass, so my experience will be specific to that, but I am sure it will extend to 1Password as well.