Supernova Civ Fleet template inconsistency

1. I'm a little bit confused about the ship template. When you start the game, you can build one flag ship, that is also your survey ship. I see here though there is still separate classes for it.

 

2. Once I had medium size ships researched, I was able to design them. The newly designed medium ships never show up on my list of ships to actually build them. I can only build the auto designed medium ships.

 

Edit: I was able to design an attack ship, but I didn't actually get to the right battle cruiser tech. It was hard to know what type of auto generated designs I was looking at. I'm guessing one of these is the siege cruiser.

 

 

3. Only one Large ship.

 

Every version of a ship I have designed for this civ also popped up when I first started it, and I had to delete a ton of stuff and basically re-do the ship fleet template.