In this article we discuss the differences between using SphinxSE and FEDERATED engine with Manticore Search
The SphinxSE MySQL plugin was made available since the first public release of Sphinx Search. The idea was to allow users to perform search queries using the same MySQL connection. Another benefit was the search result could be joined with another MySQL table for further filtering/sorting or to display data not available in the search result. Also at that time SphinxQL didn't exist yet.
Between the Manticore query and the final result to the user there can be additional processing. As in most cases, the interest is to sort by a relevance score, it's important to not lose this sorting.