Some important part properties (notably part drag, and part buoyancy) do not only depend on their shape, but also on their spawn orientation. A fuselage that is aligned along any of the primary directions will create significantly less drag and buoyancy than the exact same fuselage when rotated 45 degrees. The same is true for other parts, such as nose cones.
This is of course not desired behaviour. A craft should perform the same regardless of its spawn orientation, which is not the case due to this issue.