I'm not quite sure I'm following exactly what your question is, especially as "upload a certificate" isn't really what's happening, but I'll give it a go.
Retrieving the certificate chain from the ACME server is covered in RFC 8555 section 7.4.2, which says the default format is application/pem-certificate-chain, which section 9 describes as being a sequence of PEM-formatted certificates. While 7.4.2 says that "The ACME client MAY request other formats by including an Accept header field," the ACME Divergences document describing how Let's Encrypt's software diverges from the specification says that "Boulder does not process Accept headers for Content-Type negotiation when retrieving certificates." So I think no matter what you pass you're going to be getting a chain of PEM formatted certificates.
You are also asking about file extensions being .cer, .crt, .pem, but there really isn't a standardized meaning for those extensions or their contents. Certbot uses .pem for files that are for a single certificate, a chain of certificates, or a private key, and much other software integrating with ACME follows that convention as well. Windows tends to use .cer for single certificates and .crt for certificates intended to be used as trust anchors, but doesn't care if they're DER-encoded or PEM-encoded, they just have different default behavior when double-clicking on them (as .crt will default to asking if you want to add it to your trust store and .cer will default to just showing you, at least when I last tried them).
I hope that at least kind of answers some of your questions?