I agree with you completely. In fact, now that I think about it, I do seem to remember a case involving a company that offered cheap upgrades to the TurboTax software. The idea was that if you had already purchased TurboTax the year before, you could buy this cheap upgrade that hijacked the TurboTax engine and updated everything for the new year's taxes. If I remember correctly, the case came to an end with TurboTax victorious. I can't tell you about any appeals. I'm not sure how/if Apple can use this particular case because Psystar is cleverly arguing that their modifications are for the sole purpose of utilizing Apple's software which is allowed under some portion of the copyright law.
What's really bizarre about this case is how poorly Apple's business plan meshes with copyright law, which was created with the intent of protecting the sale of the intellectual work; Apple's business plan is to use that intellectual work to get you to buy their hardware at extremely inflated prices. This would work fine if they didn't already offer their intellectual work on a DVD. As an analogy to this thought, think of the college bookstore and how they often want to sell you the solutions manual and textbook 'set'. Unfortunately, this doesn't stop me from buying a used copy, which is similar to Apple's case.
The way I see it, Apple thinks that their software is actually worth ~$500 per copy (since the hardware in the lappy isn't worth their asking price), and is upset that Psystar has found a way to avoid paying full price. Further, they're mad that they can't profit off the hardware too. They have many options at their disposal, but since they're sleazy, they'd rather sue.
IANAL, and maybe I think my 2 cents is worth a little more than what it's stamped on, but I'm gonna give this one a try: this seems like a tactic by Apple's lawyer's to make Psystar's lawyers work harder and make the case take longer. Reading the briefs, it's evident that Apple has superior lawyers (both number and quality), as well as money to pay them with; they're strong-arming them.
From what I've read in the briefs, Apple's argument rests solely on the one clause from their "Software License Agreement" (Henceforth SLA), which states OSX may only be installed and run on Apple hardware. Without this clause, Apple would have a very difficult time arguing that the the copies are truly unauthorized; whether or not the clause is enforceable is, as far as I know, untested. I believe it is easier and less risky for Apple to drown Psystar in litigation and obfuscate the issue entirely than to actually find out.
As for the creation of unauthorized copies, they're only unauthorized if the first copy is unauthorized as well. Since Psystar legally purchased the media, Apple can't argue that discs are illegal -- simply that the copies on the hard drive are because they aren't on Apple hardware. I have a hard time believing Apple's other argument, namely that an altered boot loader and kernel extensions constitute copyright infringement, especially when 1) similar bundling techniques are routinely practiced with their Windows counterparts and 2) Apple has been paid for the software it is distributing.
I have just one question for Apple: If your computers are truly a hardware and software package, why do you bother to sell the software separately?