It's not quite obvious what all the available parameters are for convert.quoted-printable-encode. If you want the stream filter to act the same way as the quoted_printable_encode function, you need these extra params, for example:
stream_filter_append(
STDOUT,
'convert.quoted-printable-encode',
STREAM_FILTER_WRITE,
[
'line-break-chars' => PHP_EOL,
'line-length' => 75,
]
);
echo stream_copy_to_stream(STDIN, STDOUT);
Without these extra params set, you may get no wrapping at all, or wrapping using the wrong line break sequence.