I've helped pack three hundred bikes into a single trailer with Cycle Oregon and a few dozen bikes with Ride Idaho. It's no big deal. Making it more complicated than necessary will cause the problems. Some well meaning engineer will try to make it a complex rigging and space optimization exercise.
All you need to do is protect them from banging into each other and then to keep them from shifting and rocking side to side. Alternate the bikes head-to-tail if you wish but that doesn't always help stabilize anything. Simply place packing blankets or even large sheets of cardboard between the bikes. Put compressible items like duffles, tents, or sleeping bags between the last bike and the wall. Run a single tie-down rope around the whole lot.
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