On macOS use “Secretive”. It’s a small app that can generate keys from Secure Enclave and prompts you with touchid whenever those keys are being used

On iOS/ipad/(also macOS) you can also use the SSH terminal emulator Termius which has support for SE keys built in as well. So I have the set of keys synced to my VPS, this way I know that only my physical devices can log in and nothing else.