That's the thing, they can't yet.
They are proposing an attestation scheme. I'm not sure the details are out yet, but the authenticator would presumably use one of the hardware security mechanisms (like a TPM bound key) to "certify" its own authenticity along with the challenge.
This will effectively ban all open-source implementations, and end user freedom if widely adopted. Fortunately for us it seems like Apple isn't cooperating here for now, and without Apple signing on, it wouldn't get anywhere.
Attestation is not inherently incompatible with open source. Code signing keys are perfectly compatible with open source. You don’t ever commit them to the repo, if they’re even accessible to you at all (vs. in an HSM), and everyone can distinguish your official releases from forks and mods because yours are signed with your key.
Attestation is incompatible with having the authority conferred upon upstream automatically inherited by all forks thereof.
If you want your fork to have the same authority as upstream, you have to apply for that authority to be recognized and make your case that it deserves that. This is the problem with attestation: that it reintroduces human reputation authorities into the Wild West of computing.
If you’re going to argue successfully against attestation, you’ll need to focus on the actual problem rather than the distraction of source code licensing. The same attestation would be necessary whether the app you’re modding is closed source, open source, or a PICO-8 cartridge image: when attestation is in play, everyone knows you’re running a modded version, and they may choose to deny you service over that. That’s the problem attestation poses, and why arguments against passkeys fail so spectacularly to gain traction, by focusing on “open source” (irrelevant) rather than e.g. “right to be modify without being refused service”.