Just keep TOTP in your password manager at this point. Whatever security is lost by it not being a "true second factor" is made up for by not having to recover or restore backups due to a lost or stolen phone.
I would argue that the most important account to have TOTP enabled IS your password manager. So, if you already have a TOTP app to generate codes for your Password Manager why not consolidate it? Besides, if you dont have a physical and digital backup of your TOTP seeds you really like to live dangerously.
there is a base case somewhere in a backup strategy where TOTP is not feasible. The base case for me is "Keepass file backed up to multiple locations and my master key written down in an envelope in my house in case I hit my head".
Why would I lock my passwords away behind a TOTP that can get lost? My TOTP in Authy is protected by a long random key. Where do I store the key? In my password manager.
You can't use a password manager and TOTP to back each other up.