PKCE (specifically the S256 method, but that's the one that you're supposed to implement in almost all cases) is by itself a cryptographic method, but there are few points to note here:
1. PKCE relies on very simple cryptography that is hard to implement incorrectly. There is only is only one protocol defined (SHA-256), and that protocol is considered safe. Allowing the "plain" protocol in the RFC was silly, but we were lucky that the RFC writers didn't go full bonkers like they did with JWT, and started digging up ancient ciphers in case someone really wants to run PKCE on a WW2 vintage Enigma machine. In short, PKCE has no weird or old cryptography.
2. PKCE is not considered mandatory or even recommended for confidential clients prior to OAuth 2.1 (which is still a draft). It is rarely implemented in these cases.
3. You cannot use JWKS for PKCE. I believe you are confusing PKCE with the ID Token, but the GP was specifically talking about the Authorization Code flow, where the ID Token doesn't really matter. If you're using that flow an unfortunate piece of over-engineered industrial waste[1], but if you're using the Authorization Code flow it doesn't matter: even if the ID Token is completely broken, it cannot hurt you, since you must have a correct authorization code to get it in the first place.
4. Even if PKCE itself gets broken somehow (the main risk being an IdP that allows downgrade attacks), this only makes the protocol vulnerable to CSRF on confidential clients. Only on public clients that rely on custom URL schemes (such as native apps), this can lead to a more serious exploit.
[1] Sadly, this is coming from the same people who wrote the PKCE spec. On one hand they think your system might be too constrained to support SHA-256, so we need to add the "plain" algorithm, but on the other hand, they make RSA signatures (including SHA-256!) a mandatory part of the Open ID Connect spec through this totally unnecessary token.
When using PKCE the relying party can use JWKS to validate the token instead of talking to the IdP.
Are you suggesting that, that is somehow insecure?