Umm, did you even read the article? Not sure why you consider it to be an apology. There are several paragraphs of listed differences in the systems.
The article is doing what Apple's always been great at doing - highlighting minor tweaks as revolutionary changes. Xerox had proto-windows, icons, menus, pointer, scrollbars, file manager, mouse selection, etc. All of these features require way more original thought than Apple's move to menu bars, one button mice, the irritation that is resource forks, etc. Apple did do dragging right, and much credit to them for it (though I still wish the Save As motion were to drag an icon from an app to a Finder window, a la RISC OS, but I digress).
Try gathering a few facts before you make accusations.
Your language - "mak[ing] accusations" - betrays a strong difference of opinion. I think it's
good that Apple built on Xerox's work, because they wouldn't have got so far if they didn't have something great to build on. It's par for the commercial course not to list your sources when developing something, so I guess I shouldn't be too disappointed that firms don't enclose a little "with thanks to" on every product they release. Yet somehow anyone involved in academic scholarship manages it, and, as you hint, much GUI work originated in academia.
The work at PARC was based on Jeff Raskin's thesis, "A Hardware-Independent Computer Drawing System Using List-Structured Modeling: The Quick-Draw Graphics System" written in 1967. Notice "Quick-Draw"? Same name as the Macs original graphics API. Ya think this thesis had some influence on Bill Atkinson when he wrote the API?
Lol,
what? The work at PARC was based on PARC snatching up Douglas Engelbart et al. from Stanford's ARC as Stanford, DARPA, etc. got bored with him.
Meanwhile, Raskin's thesis was about manipulation of graphics primitives (so "QuickDraw"'s etymology is more specific and more appropriate than your hand-waving suggests!). While in autobiographies he likes to point with hindsight how important it was that he emphasised interactivity and hinted at on-screen menus, we are nowhere near what Xerox produced. His thesis was vaguely prescient, as any man can be by being sufficiently vague, but lacked concreteness to be influential. Indeed, Raskin had a hate-love relationship with the mouse, a topic for another mindless excursion

.
Did you also realize that Apple had already started working on a graphics project before they even went to PARC? Even on the site you linked to there's photos of progress being made starting an entire year before the trip to PARC.
The link "Busy being Born" at the bottom? The first shots are conceivably pre-PARC.
As for the sketch app shots: "I think these are perhaps a bit out of sequence, done in early 1980."
As for the sudden change to a mouse/windows UI: "It's tempting to say that the change was caused by the famous Xerox PARC visit, which took place in mid-December 1979, but Bill thinks that the windows predated that, although he can't say for sure." Considering the magnificent change, one would expect to be able to "say for sure" at least whether one's influences were internal or external, though perhaps it's documented somewhere in Apple archives that no-one's opened for decades...
Did you also miss the fact that a lot of the people who worked at PARC later went to Apple to work on the Lisa and then the Macintosh, including Jeff Raskin?
Ah yes, Raskin stopped visiting PARC to prevent "conflicts of interest", autobiography suggests, a year before he recommended that SJ go right back there to have a peek. Anyway, that people went from PARC to Apple only bolsters the argument that SJ was interested in folding knowledge from PARC into Apple's GUI - it was not mere coincidence, surely?
To conclude, Apple did great building without full chain of disclosure and compensation on Xerox (and AT&T - Unix, and IBM - PC). Now let Psystar try to build on Apple, and succeed or fail without hindrance from a paranoid giant.