Once you have worked for a Distributor & shop you will realise quality of some people’s packing. I am guessing you have never bought a bike from wiggle/CRC internet full of people moaning about marks & a scratches on their bikes. But yes it’s also QC issues also I wasn’t saying it’s all from packing it certainly isn’t but also couriers are not known to be gentle with handling bikesI don't buy it.
Repacking a new bike in another box won't cause paint runs or bubbles.
Similarly unless the repackaged box was full of rocks too I don't see how any packaging would cause damage to hard to get at areas like those shown in the pics around the bearings.
I think this is simply a decision by Orbea to ignore QC and ship bikes as fast as possible no matter what.