Buttons: interesting, but the red X throws me.
Race design: can you actually get away with not selecting SpaceFaring Race? If not I'd ax it and the (Planet Type) atmosphere settings, as its possible to get the same effect without a racial trait. And unlike SE4 GG mod you can't pick two colony types, just not enough points t go around.
Main screen- what's with the yellow hexes?
Vehicle design- spaces in the names, please.

One of the patches fixed the problem you had with them.
What are the yellow boxes? The letter codes for the ship boxes seems to have vanished, and no component uses them..
"This game thinks 100 + 5 - 5 + 100 == 0 is False" Uhh..ok?
Some of the component names are long, and the game sizes them down, making them hard to read.
What's the point of the combat map changes?
Damage Types- Internal is Internal and Armor is Armor, and never the twain shall meet. In other words, you can't have armor-piercing weapons with your current armor system. I think you noticed that already, since all the weapons use Normal damage..