If the trailer shells are locked down and the corner latches are secured properly, there should be no additional risk to the trailer. The only thought I have is if the trailer is facing backward, a heavy rain might weep into the seals where the shells meet, but I don't think it's a huge risk.
A bigger concern IMO is the main door is facing backward, and if not secured it could fly open and either get damaged or let water in. Ask the shipping company if they could seal all around the door with blue painters tape to keep it shut. It should not leave any sticky residue on the trailer.
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