I don't think there is anywhere in the ACME API that requires us to handle PEM encoding from clients. Recall that RFC 8555 specifies the CSR parameter of an order finalize request to be the "base64url-encoded version of the DER".
There is actually some Boulder-specific code that ends up enforcing that the certificate chain we serve in the response to a (POST-as-)GET to an order's certificate endpoint only ends up containing \n newlines: https://github.com/letsencrypt/boulder/blob/65e53674935b05b0b066fa60eb32892cd36acb5d/cmd/boulder-wfe2/main.go#L124-L129O
The example URLs' that @jvanasco shared aren't part of the ACME API. It looks like we should probably normalize the newlines in those static files ref'd by the website anyway. I'll file a website issue.