A lot of the tools in pixar are wonderfully clunky.
They went through a phase of hiring hip young things fresh out of MIT to write tools. Instead of nice friendly tools that play well together, they got a lot of domain specific languages.
It's been this way in the visual effects industry for decades. Most of the tools are used through a Posix layer with Perl to keep things tidy. Going into the VFX forums even a few years ago I was amazed at illustrators knowing enough Perl and Python to get the job done, because, "Designers can't code good!"
Even the commercial stuff looks like some graduate students thesis work. A basic Java GUI and about 50+ commandline arguments.
They went through a phase of hiring hip young things fresh out of MIT to write tools. Instead of nice friendly tools that play well together, they got a lot of domain specific languages.