Perhaps my most comprehensive defense of this guideline, possibly for a future revision or essay:
To the first part of what you said: as Cyrus and others have said elsewhere, the issue is that our concern is how to best serve our readers. In all of these cases, multiple formatting styles exist in reliable sources, and we are given the task of choosing one. This guideline seeks to select the formatting that best serves the readers; our responsibility is to them, not to trademark owners. In general, we believe that styles that comport with standard English conventions are superior to those that do not. If we changed the rule to say that we should always choose the style that the trademark owner uses or that most closely resembles their logo, then we run into a lot of problems. If Lego never mentions their brand name without an (r) or TM symbol, are we obligated to replicate that every time as well? If we choose to omit such symbols, aren't we already violating the rule? What about colors or font size? Just because press releases are often distributed in a black and white medium doesn't mean that Wikipedia has to be? Why not use the colors of the logo? If we choose not to use them because we find it unnecessary or we believe that it does not serve our readers, are we not making the same kind of editorial decision we've made in this guideline in its current form?
To the "naming" versus "marketing" issue, in my view, on the one hand there are easy cases, where you have something like the "tour" in "PGA TOUR" or REALTOR, which are just English words rendered in all caps for no reason other than to call attention to them. There's no naming concern there, really, just marketing. Then, from there, you have a scale, where the type of nonstandard rendering might creep away from just being for marketing and start to actually have some degree of naming as well. Is "iPod" the same name as "IPod" or "Ipod"? That's a harder question. Jeopardy! versus Jeopardy: does removing the exclamation point change the name? There aren't a lot of easy answers. However, I don't see why
The basic issue here is that for all these cases that we end up arguing about, there are multiple styles that appear in reliable sources. Our task is to develop a rule for choosing among them. We need to be clear that we're dealing with style questions, not "changing the name" or anything like it. In spoken language, for instance, "Sanyo" sounds the same whether the person speaking would write "Sanyo" or "SANYO." Style issues are distinct from factual issues. One possible rule would say that we should do whatever the company in question would want us to do. That's highly problematic, especially when dealing with trademarks, since companies like to use nonstandard styles: they're effective marketing tools, since they stand out from the rest of the text. However, readers do not benefit from being SHOUTED at or from being forced to endure end! punctuation in the middle of sentences. Furthermore, there is a neutrality concern with using these nonstandard styles: if we use "SANYO," it features their brand more prominently than the brand names of their competitors who do not use all caps. Also, there's the slippery slope: must we always use a certain color because the company prefers it? A certain font? The TM or (R) symbols? We have the technology to do that. Any willingness to not replicate color, font, or TM symbols acknowledges that we are not bound to do what the company would want us to do. The better option is the one we follow: use standard English. Words are words, even if they're trademarked as this or that or show up on legal documents as this or that. We should not use nonstandard styles to privilege certain words over others.
The full "official" and "correct" names of most companies are almost never used. For instance, the New York Islanders' full name is "New York Islanders Hockey Club, LP." Using anything other than the full name is not "official," yet it's an obvious and appropriate way to go. To that end, it would be silly to argue that "New York Islanders," without the rest of it, is somehow incorrect.