The extent to which any of this is actually implemented varies wildly between different OSes, ecosystems and tools. On macOS, docker desktop does quite well here. There's also an app called Secretive which does even better for SSH keys - generating a non-exportable key in the CPU's secure enclave. It can even optionally prompt for login password or fingerprint before allowing the key to be used. It's practically almost as secure as using a separate hardware token for SSH but significantly more convenient.
In contrast, most of the time the only thing protecting the keys in your CI vault from being exfiltrated is that the malware needs to know the specific name / API call / whatever to read them. Plenty of CI systems you don't even need that, because the build script that uses the secrets will read them into environment variables before starting the build proper.