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.
Please do consider that many software products will not change and they will still be actively used on production environments that you will never have interest about.
And it was pretty clear from the context of norir's comment that they were not talking about legacy software, they were talking about writing new projects/file formats that used newlines as a separator. Just because you want to shoehorn your legacy projects into this discussion doesn't mean that they fit.