Pixar has been using Linux on x86 for a few years now. Pixar uses proprietary software to render film (RenderMan on Linux) and around about the time Apple was licensing clones Pixar dropped the Mac Renderman port (there was no Windows version).
They build custom (Pixar-spec) x86 hardware to populate the render farms.
At the time, it doesn't strike me as strange that Jobs (who wasn't working for Apple at the time and probably wasn't all that enthralled with Scully, et al) would have concluded that Apple was going the wrong way. I don't think many people would argue that things haven't changed considerably from those dark days of mismanagement.
I would expect that sometime in the future Pixar will upgrade hardware and may even port RenderMan to OSX, but they are in business to make money and don't just buy new gear 'cuz it's cool, so time will tell.
I don't think it's a coincidence that Apple under Jobs has begun to agressively challenge x86 rackmounts with the Xserve.
Pixar also uses Sun and Apple hardware, but not for rendering. Prior to the Linux port, Renderman ran on SGI hardware.
Note: I wrote the above before I could find the article (your link only gives me a banner ad) but did find it by the old "cut the tail off the url trick" here:
PCPro
... then going to the story at right:
Pixar Picks Linux
I am a bit puzzled about the information in the story, this is not new; it appears the story is based on stuff I read years ago. For example:
Pixar drops SGI for renderfarm
Note from the story that 2 million lines of code ported at an average 2,000 lines per day. This means the decision to go Linux on x86 was made at least 1000 days prior to SE 2001 (assuming coding began the same day the decision was made).