Integration with TinyMCE breaks TinyMCE formatting

In wysiwyg_filter.module the function wysiwyg_filter_wysiwyg_editor_settings_alter
passes the settings to the TinyMCE module. Passing over the settings breaks TinyMCE formatting (e.g. all inline styles are stripped off - altough the directive @[style] is set for the WYSIWYG filter).

Additionally, the Drupal way of filtering is doing it while the content is viewed and not when it's stored. Altough I think that it's valid to do such stuff in TinyMCE it may not be a good idea for a filter to do such stuff because developers won't expect to do it ?