A difficult one this.
If I use a ferry, I tend to put it in gear, block the front wheel and single strap over the seat. If they go on a trailer it is chocked on the front wheel and they savagely tightened down by straps on the front to compress the forks and tied at the back to stop the rear swaying.
I would go the trailer route but be careful how much "welly" you give the front straps. Sometimes people seem to want to bottom the forks out or pop the fork seals. Can you get a front wheel chock? LINKY this will stop the wheel from wanting to turn left or right. It also allows the bike to stand upright without a stand. Then tied down at the front with ratchet straps until the front is compressed. One over the seat - use some padding on the seat so that the strap doesn't eat into the seat itself. Then a couple of straps at the back to stabilise the rear. Work front to back.
Straps are cheap, bodywork isn't.
Then the daily panic until you re open the crate.