New player here, confused about what I'm seeing on my Terran ships.  It seems that premade ships are rigged and/or bugged, ruining the integrity of the ship design concept.

I have the option "Remove functional components when upgrading" turned OFF, so I see what's on it. Seems like the kind of option that would be ON by default, but now I see why it isn't.  On my Terran Phoenix M5, I click Upgrade and I see:

1.) It's carrying 48 'size' worth of components on a size 33 hull (Small Hull with some Mini techs researched).  Further, the 'size' bar at the top says 40/33.  Huh?

2.) It has a Plasma weapon equipped which I haven't even researched yet.  Huh?

3.) It has 11 laser attack worth of weapons (the one Plasma & eight Laser Vs), but only 8 attack showing in the ship info.  Huh?

4.) It has two Superior Deflector sheilds, and zero defense showing in the ship info.  Huh?

Why? 

This makes it almost impossible to intuitively upgrade pre-made ships when I research new techs.  And when I choose to make new ships from scratch, it makes comparitive analysis of pre-made and custom-made ships a huge headache.

Yes I can and will make my own ships, but when ship tech and ship design are arguably the core of the game, this huge disconnect between pre-made and custom ships is very poorly concieved.   Major game design foul.