Very interesting question, I have no experience here. What I do instead is scan my QR codes into two apps on different devices when I make them (I do not make them very frequently so it's not a chore). Because I'm sort of pessimistic after a lifetime working in tech - everything that uses electricity breaks and fails. I build redundancy into all my (things) and just expect one of them to fail. Goes for email providers, hard drives and OTP codes - if I could have a backup washing machine, I would. :)

Aegis authenticator backups can be imported into Gnome Authenticator. I'm using it, I know it works, but I don't recall the format GA requires

I just copy the OTP-URL from Aegis and place it into pass (passwordstore.org, with the pass-otp extension) on my desktop computer. That pass instance is backed up along with everything else which matters.

If you move the secret tokens onto the same device (like in that emulator that presumably runs where your password manager also runs), we're again back to the oathtool solution that is described in the OP, that doesn't have the same security benefits as the original intent of supplying you with a 2FA token. Not saying you shouldn't do this, just something to be aware of when you use the export mechanism in this way

1. Aegis has a setting for creating secure backup on every change. 2. Autosync that backup directory via syncthing to your PC. 3. Run a compatible desktop software (e.g. linux has authenticator) to import aegis backup files manually.

Since totp addition is not a frequent activity, the last manual import step was not a hassle to do whenever needed.