Are bikes not fully assembled and shipped to the dealer that way? I don't understand why the manufacturer would take it apart after it leaves the assembly line and have the dealer reassemble the unit when it arrives.
Things that protrude too far into nothingness (IE, making the crate bigger than might otherwise be necessary, air costs just as much as actual weight to ship) may be removed - mirrors, overly high windshields/fairings, handlebars. Based on what I've seen anyways...
Just getting the bike unpacked and safely out of the shipping crate can be a 20-30 minute experience alone, having seen it done.
After getting it out and bolting anything back on that was removed, the inspection should catch anything damaged in shipping. Most people think that shipping is a gentle process - box is loaded onto truck at the shipper and it proceeds directly to the dealer. Reality is that it may go through many transfers and different trucks along with crossdock handling between A and B. Forklift damage, shifting freight damage, just plain old bouncing around in the trailer...all can potentially cause issues.