Noticed the same thing with my big shipyard. although a bit less severe than yours.
Not sure how "fixable" this is, it's just collision detection that brings your performance down.
This only happens when you're in ship mode, so maybe this doesn't need to happen in *docked pilot mode*. Even if it was moving around on a rail, pilot mode has no effect on it. Maybe it's doing collision detection as if the ship was undocked?
The example blueprint has huge docked shapes slide inside each other which would wreck havoc when undocked, and you're noticing the same thing when sitting in pilot mode in a docked entity.