We are keeping an eye on things to monitor the extent of any breakage due to this change. So far, we have observed very few domains continuing to serve the X3 intermediate in their chain despite having gotten an R3-issued end-entity cert during their scheduled renewal. For those few domains where we have observed this failure mode (which is not necessarily a full breakage: browsers may still be able to verify the end-entity cert despite the wrong chain being served), we are working on determining commonalities so we can reach out to the appropriate ACME client developers.
Note, however, that even APIv1 ACME clients which do hard-code the /acme/issuer-cert API path rather than getting it from the <link rel="up"> attribute are not broken by this change: we changed the cert which is served at /acme/issuer-cert from X3 to R3. The only clients which would be broken by this change are those that bundle the intermediate cert directly, fetch it from a hardcoded non-ACME url (e.g. from the AIA url), or fetch the intermediate upon first issuance but then ignore it during renewals.