It doesn't sound like you are making it as far as where this would have an effect, but what version of CTAP is your yubikey using? For this setup you will want to make sure your key is using 2.1. It's possible 2.1 PRE will work, but I can't confirm. For digging further into your troubleshooting, you will probably want to look at sites that are security focused as I don't think security at the level you desire has made it's way to this type environment/forum yet.
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