Certes.AcmeException: Can not find issuer 'C=US,O=Internet Security Research Group,CN=ISRG Root X1' for certificate 'C=US,O=Let's Encrypt,CN=R3'

I think that bug report in Github is wrong and might need to be corrected.

"This change involves not returning the root certificate with the request (short chain)."

The report reads to me as if the OP in that thread is under the assumption the (Cross-Signed) X1 is functioning as a Root Certificate, when it is actually functioning as a cross-signed Leaf Certificate.

Many of the bug reports and issues on this topic, across multiple clients, seem to stem from the same misunderstanding. See also: Chain incomplete since feb 8 2024