I don’t think you are missing anything. Make sure your BW vault is super protected.
I see a difference between a passkey stored in BW and a passkey stored on a yubikey (with a PIN that wipes the key if you get the PIN wrong too many times).
I wouldn’t be suprised if websites (maybe called relying parties) start to differentiate between these 2 cases or if BW add a PIN to the passkey but that is only my thought.
I think any future changes should be led by the FIDO standard.
I don’t store TOTP secrets in BW, so I personally am not comfortable storing passkeys in BW, except for websites that actually allow 2FA additionally to passkeys.
For people who do, passkeys are better for the 2 reasons you said.
I heard on reddit that BW is considering putting in another PIN for passkey, but I can’t find the post.
For people using strong random passwords + security keys for BW, I can see the argument of storing both (TOTP secret, passkey) in BW for simplicity sake (backups, emergency access, etc.).