You're very sure about yourself. Good for you, I can absolutely appreciate that.
But unfortunately, even though this is the internet, any amount of confidence you throw at this doesn't make what you say any less incorrect… ;p
The number of physical labels Schiit slaps on the boxes has no direct correlation to how shipping is calculated or how it's billed to them (and ultimately to you).
Purchase two Tyrs in two separate transactions, and Schiit's shipping retailer will bill Schiit for two completely separate shipping transactions, one box/label each. That part you've got completely correct.
Purchase two Tyrs in one transaction, though, and Schiit's shipping retailer will bill Schiit for one shipping transaction that will consist of two boxes/labels, one "master" label and one additional piece that will belong to the same "master" shipment.
Wanna know how I know?
Because I can read FedEx's tracking info for my Tyrs:
Why does this little distinction matter?
Well, because it completely changes the way FedEx evaluates what you're trying to ship with them. In the first case, they see one single box of 50 lbs. Nothing outrageously heavy, nothing weird, so all is well.
And then, a little bit later, they see another single box of 50 lbs with no relation to the first one whatsoever. So, again, nothing outrageously heavy, nothing weird, so all is well.
Next, let's try to ship these two 50 lbs boxes in one single transaction. Now FedEx sees a shipment with a combined weight of 100 lbs. "Wait a sec!", they say. "That's a lot of weight! We'll charge you extra for that Schiit."
"But guys!", you say, "It's two boxes of 50 lbs each! It's the exact same work for you as if I were to ship them separately! Why do you charge me more?!"
"Well, because it's 100 lbs! And also because we're FedEx, it is well known that common sense does not apply to us, so… ¯\_(ツ)_/¯"
I hope you understand that I am not arguing against your point; shipping two separate boxes should cost the same regardless of whether they're combined into one shipment or shipped as two individual ones. It's the same weight, the same boxes, the same amount of physical work FedEx has to do to get the job done. So it makes no sense that the combined single shipment costs almost 40% more than if you were to ship them separately. To the contrary, it should be slightly cheaper, as there's slightly less organizational and financial overhead involved when you treat them as one shipment.
I'm simply saying that your intuition, as logical and as sound as I agree with you that it may be, just doesn't reflect how it actually works – and that it's not Schiit's fault that it is this way, which is why I decided against doing what you rightfully did; to ask for a refund of the difference. That's all.
What Schiit
could do is to change their approach to how they send the request for the shipping quotes to their shipping retailer by treating every Tyr in your shopping cart as a separate order. But I'd be willing to bet that neither their current e-commerce implementation nor that retailer's APIs would support that out of the box and without some larger changes to the shopping cart's source code.
Another approach would be to enforce that you can ever only buy one Tyr per order. That's probably a lot easier to implement.
But I'd also bet good money that this will cause more harm than it would help because both solutions just end up being confusing as heck, and they'd have to explain why it's this weird dozens if not hundreds of times over to confused buyers when all they want to do is to buy their freaking amps, and not bother with why stuff is limited to one per order, but not one per person, and why things gets split into multiple shipments, etc.
[Edit]
And then there's the case where FedEx wakes up one day and decides to change things up a bit and charges less for a combined shipment all of a sudden than for two separate shipments. Now you're forced to play cat and mouse with them to always ensure that you're offering the cheapest shipping method to your customers. Or what if one and the same shipper decides to bill 40% more for a combined 100 lbs shipment when shipped domestically, but 10% less when shipped internationally? Then you have another edge case to plan ahead for and test on the fly in your e-commerce implementation.
[/Edit]
The way it is right now, albeit a bit dumb and seemingly unfair, is actually probably the best way to do this, and then just eat the occasional refund request because the alternative is a lot worse, or at least quite a bit more expensive.
If you want to complain about someone being a total idiot, complain to FedEx. They deserve it – on more than just one level… ;p