I don't know how JS organizes their inventory, but at boutiques and ADs, watches are often stored separately. When I bought my first Omega, they showed me the watch that had just arrived that morning in a plastic "coffin", then pulled out the special box and full packaging as I got closer to buying. It was stored in a different part of the store.
Similar situation when I purchased a Rolex. Never saw the actual box until the purchase was almost complete.
Yeah, OP should not be wearing this watch if this transaction is truly a horror.
Me, I wouldn't categorize this as a horror story (it's easy to find much worse real-life stories with no hope of fair resolution), but it is disappointing, and would likely dissuade me from dealing with Jomashop if it is not resolved to some degree.