Just a thought -
I'm not familiar with Mr Scharphorn's methods, but could those (countersunk type) holes be the result of partial assembly to line up the panels and drill the pilot holes?
If that were the case, when asked about the "countersunk" holes, he would have answered, "Oh, we screwed in a few to line up pilot holes on the connecting panels." ...or something to that affect. Their presence would not have been such a mystery. Also, their would have been matching holes on the other cages instead of just the first one or two.
As it is...based strictly on what has been posted here so far...I see a moderate lack of diplomacy on the buyer's part resulting in a severe overreaction on the seller's part. If the buyer had just accepted the "mystery" of the countersunk holes and focused on the real problems of the shipment, he MIGHT have been able to at least get the missing parts shipped in a timely manner, and maybe even worked out some sort of replacement for the damaged panels. Instead, everything quickly dissolved into a "Did TOO!" "Did NOT" sort of playground argument.
Although, based on the seller's attitude, it appears that any extra step he might have to take to make a customer happy is simply too intrusive, because obviously none of it could possibly his fault.

(That's how it looks at this point, anyhow...I've noticed the seller has yet to chime in on this thread, although he was awfully quick to respond to the previous comments made in other threads.)
I'll go on record as one of those people who will NOT do business someone who has such poor business sense and a quick, nasty temper...no matter how "quality" the product is. I'll pay more for the security of knowing that IF there is a problem, the company I'm doing business with will work with me in a professional and courteous manner.