The ISRG root certificate is currently not included in most root programs. For that reason, Let’s Encrypt currently defaults to using the issuer certificate cross-signed by IdenTrust, which leads back to DST Root CA X3. Once the ISRG root becomes trusted, this is bound to change - server operators will be encouraged to include both issuer certificates. Right now, this would essentially be wasted bandwidth because the majority of users won’t trust that root certificate.