Current signatures:

generate_text_for_storage(&$text, &$uid, &$bitfield, &$flags, $allow_bbcode = false, $allow_urls = false, $allow_smilies = false)

parse($allow_bbcode, $allow_magic_url, $allow_smilies, $allow_img_bbcode = true, $allow_flash_bbcode = true, $allow_quote_bbcode = true, $allow_url_bbcode = true, $update_this_message = true, $mode = 'post')

generate_text_for_storage() supports the following toggles: allow_bbcode, allow_urls, allow_smilies. All set to false.
message_parser::parse() supports: allow_bbcode, allow_magic_url, allow_smilies (all three required parameters) plus allow_img_bbcode, allow_flash_bbcode, allow_quote_bbcode, allow_url_bbcode, which default to true.

I propose to add those four extra parameters with a default value of true to match current behaviour.