I think the article mixes up several different problems. Both cryptographic keys and opaque tokens are "possession factors", i.e. if you have them you can authenticate against a service. Signature-based authentication schemes are mostly used to protect against replay attacks, which are easy to perform with an opaque token as it won't change.

That said you can tie both opaque and cryptographic tokens to additional factors. For example, machine tokens can be tied to specific IP addresses, so an adversary won't be able to use them from a different device. Tying them to other possession factors like TOTP codes would also work, though it's often impractical.

Mobile apps can easily make use of signature-based authentication schemes based on keys stored in a secure enclave, both Apple and Android phones have good support for that. For web apps it's more complicated as there's no way to store keys in an enclave (and many older laptops/computers don't even have TPMs), so you keep them lying around in memory or in the browsers' session/local storage, which of course isn't ideal.