Right, but I can't require a second factor on a different device that operates outside of my primary device's trust store. I'm sure there is some way to make my desktop hit my phone up directly and ask for fingerprint auth before unlocking the local keystore, but that still depends on the security of my device and my trust store. I don't want the second factor to be totally locked to the device I'm running on. I want the server to say, "oh, cool, here's this passkey. It looks good, but we also need a TOTP from you before you can log in," or "loving the passkey, but I also need you to respond to the push notification we just sent to a different device and prove your identity biometrically over there." I don't want my second factor to be on the same device as my primary factor. I don't know why a passkey (potentially protected by local biometric auth) + a separate server-required second factor (TOTP or push notification to a different device or something) isn't an option.

EDIT: I could make it so a fingerprint would decrypt my SSH key rather than what I have now (i.e. a password). That would effectively be the same number of factors as you're describing for a passkey, and it would not be good enough for my organization's security model, nor would it be good enough for me.