I haven't touched the dev build yet, do you have to go through a connected shape to be able to jump?
I think it's only the core which has to go through.
My fat puddle jumper (17x 9y 21z) could use the gate even though only the front (11x 9y 21z) without expanded missile-pods fit through.
* Positive effect: Could encourage peoples building bigger behind their core, not to build doom-cubes.
Thinking about it, I've got an idea. You could build a ship which has a J-shaped front. Your core is still protected (from most angles) but you can rotate through the gate... have to try it NOW