For the record, I am not a lawyer, nor do I have detailed knowledge of laws on Intellectual Properties and such (e.g. copyright, trademark, etc.). Not surprisingly being online enough and a member (at least casually) of several "fandoms", I also know that such laws are fiercely debated.
PokePop: I am familiar with Disney, and avoided bringing them up because quite frankly, their overzealous actions in this area have earned them quite a bad name in many circles. After all, Disney has gotten at least a few laws on "Intellectual Properties" expanded, to avoid their earlier works becoming public domain.
This would extend this side discussion to yet another topic. The discussion was first about the seizing of counterfeit cards. Now it seems to be about proxies and their legality (at all, not just for OP), and now we are getting into something I briefly alluded to earlier, whether some "laws" are actually just, in essence whether they are true laws or not.
For the record, if someone told me that a company was tolerating proxy cards, I would indeed define that as "ignoring them or giving a choice to the local organizers and judges about whether or not to allow proxies." Not trying to be flippant, just pointing out as such I really don't grasp your point.
This likely is due to different understandings of what "tolerance" is. To keep it short, I tend to go with the definition "the act or capacity of enduring; endurance". Being "neutral" or even "encouraging" towards an idea is not tolerance as I understand it, though it certainly is used that way by many modern groups.
PokePop is right in stating that companies must be selective in how they enforce copyright laws; it takes time and money to enforce such claims, so there often simply isn't enough resources to stop every violation. There is also, as I stated earlier, much disagreement over those laws and how they are enforced. Disney caught a lot of flak over the above daycare incident, and long story short; even if the law is on the company's side, public perception isn't. This isn't some core conviction clearly expressed by long held moral beliefs (e.g. religions), so public opinion matters to it greatly.
The fact that companies have to worry that allowing one person to skirt the law sets precedence for all too is unfortunate, and a failing of the American legal system. A bad court decision shouldn't change laws, and one act of tolerance shouldn't negate a person's rights. Disney allowing a daycare (even a for profit one) to have a mural depicting some of their trademarked characters shouldn't preclude Disney from preventing someone from setting up a business built expressly by violating their intellectual property rights.
nopoke: I know you were addressing deashira, but I've got to ask is this a good, competent lawyer who understands exactly how the American legal system works, or how it is far too often practiced? Seriously, we need legal reform here so that companies aren't forced to be cutthroat or ignorant of people using intellectual properties for private, not for profit use, especially as a part of using that hobby. With the TCG industry being built on "artificial" rarity that would be illegal for other products. In a system where unfortunately so many rulings depend on precedence, if I were a lawyer, I would not want to wish a sympathetic judge or jury who might ruin my current business model. Unlikely, but so have been many other rulings. >.>
Also, you haven't refuted my point that one of the uses of the World Championship decks is as a proxy to enjoy the TCG in a non-tournament setting. While they are clearly not legal for tournament play, and may not even be legal for League play (last I knew that was up to whomever was in charge of the League), they had better be legal for home play or else we have a major situation. Not one without precedent (I am using that word and variations of it far too much this post), but I am still pretty annoyed that I technically don't own any movies, games, etc. that I've paid for a hard copy of, but rather the disc, cartridge, etc. is merely a "license to use" said product.
tl;dr: So yes Pokemon (and indeed, many companies) don't prosecute every violation, for their own sake; its too expensive and would drive many customers away. IP laws are really messed up, and far too many in the legal system believe that legal precedence trumps actual law.