I'm running into this same issue. Not only does it open the native iOS Password Manager, it won't allow you to add a new account.
You always have to add it to an existing account, which means that any user who doesn't have their login credentials already stored in iOS Password manager, they're unable to setup 2FA with this link.
Is this expected to be fixed in iOS 15? Is there something else we need to be doing with the otpauth urls?
I'm running into the issue with this URL as a sample:
otpauth://totp/github.com:?secret=&issuer=github.com&algorithm=SHA1&digits=6&period=30
(you can repro by clicking on this link from Notes app or iMessage app)