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The problem is not the RSA math itself but that it is both extremely slow and implementing it is particularly susceptible to bugs and side channel attacks https://blog.trailofbits.com/2019/07/08/fuck-rsa/
Most of the situations I encounter RSA are in projects where I hope RSA is implemented correctly. I have a lot of Let's Encrypt certs that are still RSA and my main SSH keys are still RSA. All of these were generated quite some time ago. I understand the problem with projects that implement it incorrectly but I'd hope OpenSSH and certbot aren't those projects 😥
For Certbot, I think it's even further up the chain - OpenSSL. And if you're installing it to Apache or Nginx, its probably just OpenSSL again.