Imi, if you see in the photo of my bike just out of the box (or before, I forget) you'll see that I brace the tire up against the bb area of the non drive side. With some padding between the wheel and frame to stop paint getting rubbed off, I tightly zip tie the wheel at two or three points up against the frame , one up by the headset.
I'm fairly certain to say that having the crank near the wheel as you suggest would put the wheel at more danger, and take up more space---I can say with 100% certainty that I've always only seen brand new bikes just removed from a box only with the front wheel on the non drive side (a few times bike store owners have been really friendly and taken a new bike out to give me the box, so I could have the right dimensioned box--but they were going to build the ibike up anyway, so it was going to come out anyway)

If manufacturers do this, I reckon that is the proof its the most efficient and safe method.

what I like with the non drive side is that the protruding bb shell area means the wheel is fairly "flat" against the frame, so less "bending" or forcing forces going into the wheel if suitcases are piled on top of the box if it is laid down on a cart or something -- I always recall getting off the plane in Portland,Oregon to ride down the west coast of the States, and seeing out of the terminal window my bike box unloaded off the plane, placed on the bottom of a cart and then the guys piling a whole load of suitcases on top of it......