Yes, I can see why orthogonal was a bad choice of words here.
Here's my point: those things mentioned were improvements on things that didn't work very well even for trusted applications that did nothing unreasonable.
When your development environment or even regular desktop software spreads itself all over the filehierarchy as a matter of practice, conflicting and interfering with every other application because it does the same thing, that's taking something that used to work just fine and breaking it. Then you add a layer of abstraction like containers to solve the mess you created.
Containers are a good idea for a lot of things, I just don't think I should need them to run normal everyday software.