One notable option for people who encounter a difficult to solve conflict regarding the certificate chain is of course to use an alternative ACME CA, of which there are now a few to choose from and in most ACME clients you can mix and match depending on your requirements. Most are summarized here: https://docs.certifytheweb.com/docs/guides/certificate-authorities#supported-cas
Most users should be happy sticking with Let's Encrypt but I wouldn't want anyone to see this issue as an insurmountable problem and I don't think LE would either.