The E1 chain is just some intermediate(s) terminating at either ISRG Root X2 or ISRG Root X1.
Compatibility-wise, it is no better or worse than requesting the current R3 alternate chain (terminating at ISRG Root X1).
E1 will never replace R3, because they use different algorithms. R3 is RSA, while E1 is ECDSA. E1 is exclusively for ECDSA leafs, while R3 will in the future be exclusively for RSA leafs.
The only thing that will change is the current option of obtaining an ECDSA leaf signed by R3 (which will be removed at some point).