The supplied ships have extra components which are purely cosmetic.  If you take them off you'll likely notice that no space is actually freed up.

Design focus allows you to specify the type of weapons and defences you want the computer to auto-design onto ships.  It likely will not include any extra stuff though, so this option is just there if you don't want the hassle of designing ships and just want to focus on the rest of the game, which is fair enough.  Your best results will always come from focusing on one damage type and one defence, as not only does this use space most efficiently, it is most effective against an enemy which has no defence against your weapons and uses weapons that you are defending against.

That said, designing ships yourself allows you to take advantage of components like engines, hull strengthening, and fleet-boosting modules.

The game-designed ships get to cheat in space-usage, it seems by about 20%; probably to compensate for the human players' strategic design skills.  

I often use the focus button in the shipyard as I build early small ships; if you focus appropriately for your research and needs, you can get better simple warships than you can design yourself.  Once things become more complex; if you need drives, or use modules, then you need to design 'em yourself.