It makes writing parsers more complicated in certain cases because you can't tell without lookahead if a newline character should be treated as a newline or an eof.
I won't mention telnet because you don't use it, but in CSV and similar data it is quite a trouble to normalize the data. So instead of 2 possibilities now we 3 to detect.
I don't get the CSV part. You can emit a new row after a line ending and on EOF with non-empty buffer. What's the tricky part or third option here? The crlf is never a part of the data.