I think it will be down to the way the seller handled the situation.
To use your example of the speakers we would need the speakers and stand to be sent in separate boxes. The sellers would then need to claim the courier has lost the item. But you would then provide proof that they were never sent. Then the seller would say, No worries i will send out a replacement item and then 3 days later they then turn around and say infact I will give you a refund at around 1/3 of the value of the missing item as we no longer have the item in stock. Only for you to then find that the item is in stock.
If you were Ebay and you saw this you would be worried about the impression this seller gives to the buyer on the entire ebay platform. So they need to "punish" the seller. I'm sure if they had attempted to handle it better they wouldn't of been penalized as much and they would have just been forced to pay return postage and give a full refund.
Agree you'd hope eBay properly investigated this and didn't just default fire a refund to the buyer without considering the nuances