For the most part SFA uses 3rdR and Imperial Starfire.  In addition, to this is the changes to Imperial Starfire introduced with Sky Marshal 2.  Plus you get the technology from Alkeda Dawn and with SFA7 you get the UTM (possibly that showed up in SFA6).  When you start a game there are other options available to the player they can set (-1 to all PD rolls for example).  There are also experimental optional rules which Starslayer and I are using (supply lines and mine laying systems).  There are also setting to adjust things like growth rates, and cost of technology.  The database is also available to be edited if you have the access 2003 program, the skill and the password to allow you to have house tech. 

Overall there are significant number of options available to the SM for the game.

There is no way to not use the core rules (3rdR, IS, and SM2) as these are programed in.  They are used for race generation, system generation, the tech available per EL and the combat resolver.