Get a plastic spacer to put inbetween your forks so they don't get crushed. or use a spare hub / axle / whatever. The bike shop should have shit loads, just ask for some.
My stem was resting on my toptube (with bubblewrap in between) when I went away, and it dented the top tube. However, that was on a Koxx Sky which has major thin tubing. Watch out for any sharp or cornered objects that could interfere within the box, or pierce the box.