@fzp, welcome to the commmunity! 
According to the announcement
for the time being you should register your account that the leaf certificate you generate would be signed via ECDSA signature. However, be aware that unless the ISRG Root X2 certificate is in your trust store (mostly not the case yet), the ISRG Root X2 certificate will be cross-signed via ISRG Root X1. And that is the same situation as you described originally; an ECDSA certificate with RSA signature. The good news is, that it does not affect the TLS negotiation, unlike the case of leaf certificate.