I run a cryptography forum, I know this stuff, and the problem isn't algorithmic weakness but complexity of implementation.
All major browsers and similar networking libraries now have safe implementations after experts have taken great care to handle the edge cases.
It's not a fault with let's encrypt. If they allowed nonstandard curves then almost nothing would be compatible with it, even the libraries which technically have the code for it because anything not in the TLS spec is disabled.
https://cabforum.org/baseline-requirements-certificate-contents/
CAB is the consortium of Certificate Authorities (TLS x509 certificate issuers)
With that said curve25519 is on its way into the standards