Sorry to resurrect a dormant thread but I'm having this issue as well with the Ultimate edition. The Custom ship box is always greyed out. Strangely enough it was working at first, but i've no idea why it's stopped. I've only really been playing the TA chapter and when I have looked at the other chapters I've always set it back.
I've only had the game a coulpe of weeks so I imagine it's quite possible that I've changed an option somewhere.....what that might be I have no idea.
Any help would be welcome.