I got seriously annoyed when (at later levels) the ship's hitbox inevitably becomes ridiculously huge. Fortunately, that was easy enough to fix. (broken image removed) NOTE: I tested with an alt account on Kong. Ships with overlapped parts save, load and behave perfectly. (broken image removed)
Ship parts allowed to overlap (2 results) (Updated June 29) (Tested July 2 and still works)
26 68 90 0a > 27 68 90 0a
The developed tried to stop overlap/limit-bypassing exploits, and I made this really quickly so it's not really identical to the previous one. You need to have one spare unused part in your inventory to build an overlapped ship. What you should do is build the overlapped parts as usual, then take any spare part, move it around but don't attach it to your ship, then you should be able to reconstruct with the overlapped parts.
[spoiler=outdated:1a25fugb]Ship parts are allowed to overlap
26 68 f6 07 > 27 68 f6 07
o_o (At phren's post) sorry.