I thought this bug was fixed in 1.99rc?  Should be fixed in 2.0 as well.

If you're curious, the reason the autodesigner makes ships like that is because it failed to account for the current level of miniaturization.

this is not fixed for 2.0...at least not mine.  if you leave the components on when you customise them you can go to delete them individually.  what you will notice is that certain components need to be removed twice to be removed....its like two components are superimposed (the icon) so it looks like only one component is there but there are the effects of two.    the component will go away on the first removal but its icon will stay and the space available will not change.(the effects of the component are reduceed however.)  removing the icon a second time results in the space available increasing and the icon dissapearing.....

in effect its like the game squeezes two components into the space of one....

Now this is annoying to me because I enjoy upgrading my designs by swapping components as my technology improves.  thereby I have slightly different ships at any time and can  make small improvements as I go...but I can never sqeese in components that way so it makes that an innefective strategy....

 PS I dom't undestand why everybody sys this is fixed when none of the change lists list it......I think no one notices because they use the auto remove option  but this is just a theory of mine....

but still please go in game and attempt to upgrade  design  without the auto remove components option then  remove one component at a time and pay attention to the affects...there is something fishy.......

Have you looked at the stats when doing this?  I remember a while back a clone/phantom colony module was put on the default colony ship to make it look better (symmetry and all that), i.e. a module that looked like the colony module but didn't actually hold any population, nor take up space.  It wouldn't surprise me in the slightest if that's how the premade ships, or even autodesigned ships, are now.

If I'm understanding you correctly, I would recommend you reinstall your game.  It is definitely not supposed to be like that, and I can't seem to replicate either what you're seeing or the original bug in my game.

Interesting.

Fired up the Terrans and let the game autodesign a ship for me, wound up with Star Fury M1.  (To my knowledge there are no longer premade weapon ships in TA.  If you are still able to see premade weapon ships without using the autodesigner, tell me how I can get there so I can compare.)

While I am in fact able to see a second laser on the tiny hull (and there's no way in hell it would fit), it does not take up space nor does it contribute to the attack value.  This is the case regardless of whether or not I have researched Laser-at the time of the initial test I only had particle beam via space weapons.

I also see a support module and a sensor module on the ship design, that do not take up space nor give the ship design, even in the shipyard/ship designer, any bonuses.  I'm seeing 2pc sensor radius and 0.1 sct range both before and after removing them.  (Tiny galaxy for testing purposes by the way, in case that range seems low.)

The interesting part is that when I go to actually build the ship, the only component on it is the aforementioned particle beam.  The phantom laser that isn't providing any attack doesn't show up, and the basic support and sensors don't show up, either.

I think this is intended for the looks. I guess it uses some template with phantom components and adds real but invisible components on it.

I hope they fix this again in the next update. Using such designs makes the game too easy.

I noticed this as well, there were excessive components listed when I hit upgrade on the basic Constructor.  Not only that, but several of the components weren't even allowed by my technology level.  There were range and sensor modules on it well above what my starting techs permitted.  This wasn't quite game-breaking, as none of the components actually imparted stats, volume, or cost to the ship design.  They were, for all intents and purposes beyond the rollover popup, eye candy Extras.

I'd like to do this myself.  While most actual parts aren't that impressive, some do have a nice look and would go well in my standard templates, if I could add them as extras instead of components.