section 31 is no top secret research agency. some fan sites made that out of it

to follow the secured startrek sources section 31 was a part of starfleet, an special group to protect the federation. cause this paragraph has been removed sometime before ds9 from the UFP agenda section 31 is now an illegal operation.
We don't know much about the Star Fleet Intelligence. It seem to have it's own structure (i think picard said sometime 'a commander from the Star Fleet Intelligence', so you can think they have their own ranks). It's not sure if they have their own star ships or fleets, but at least they had the USS Incursion in ST-Away Team, so that can be seen as semi-official

For the Fleet Operations universe we followed what we knew about the SFI; so they have their own structure and are an small, independent part of the Federation, just like Starfleet.