I believe that the base64 implementation in coreutils should ignore carriage return and line feed line endings (CR, LF, CRLF). Currently, it only ignores LF line endings.

The -i/--ignore-garbage flag is effective, but should not fail on common line endings.

$ echo -ne "R05VIEJhc2U2NCBkZWNvZGUgc2hvdWxkIGlnbm9yZSBib3RoIENSIGFuZC9vciBMRg0K\r\nR05VIEJhc2U2NCBkZWNvZGUgc2hvdWxkIGlnbm9yZSBib3RoIENSIGFuZC9vciBMRg0K" | base64 -d
Current Output:
GNU Base64 decode should ignore both CR and/or LF
base64: invalid input

Expected Output:
GNU Base64 decode should ignore both CR and/or LF
GNU Base64 decode should ignore both CR and/or LF

Per the Base64 RFC, section 3.3,

Note that this means that any adjacent carriage return/line feed (CRLF) characters constitute "non-alphabet characters" and are ignored.

https://tools.ietf.org/html/rfc4648#section-3.3

My interpretation of this section is that the base64 decoding should either fail on any non-Alphabet character, or should ignore any line ending combination.