I never use the auto designer, so I can't tell you what's wrong with it. However, you don't have to let the computer do the designs for you, you can also do it yourself!

You can choose to create a new type of ship altogether (in which case you'll be modelling how it looks, as much as what kind of weapons it has), or just improve on an already existing template.

Either way, you go to the Shipyard and either select "New" or select an already existing ship and select "Improve". With improve you'll be given a ship with the same look as the old one, but without any of its functional components, you can then add weapons and defenses for as long as they'll fit. Save it under a new name, and presto! There's your mass driver/armour ship. If you select "new" you can also select what hull size (and thus how much will fit on the ship) you want. Be aware though that the Cargo hull size has a lot of room, but only one hp, which makes it a terrible warship that will lose pretty much any battle.

Usually, you are better off designing your own ships, rather than letting the computer do it for you. Good luck!