Hahahahaha
Yes it is impossible to add modules to those ships lol... lots of shrinking required.
I forget if the "hide part" command works on real components... but if and when it does that would certainly make things easier. Otherwise... well... sorry 
@Ashberry76
Well, that is a good question. In general, I intend for my mod to not alter gameplay in any way, so that I can make it as compatible as possible with all other mods, I think Deathwynd is working on something with Ship Blueprints and thus why he needs to make 9 more designs... but other than that, you can add this to any other mod hopefully.
Immediate Future goals are:
1) Flesh out each ship set (in some cases I got lazy and repeated the same ship model too often)
2) Add fun names for each ship in the descriptions
3) Add 3 more Ship Sets and custom races.
4) Learn to add/mod Minor Races (though with so many opponents allowed, I'm considering why have Minor Races in a game at all?)
5) Learn to make quality logos and start adding those.
Notably, if anyone is already really good at logo making and wants to assist, I'd welcome it. I'd only have specific wants for one logo, and all others would be entirely up to you.
PS: Is it just me, or Logos kind of... suck on the galactic map? They are always so fuzzy and illegible, I wonder why we bother having them on there...