Shouldn't computer skills courses be prerequisites for programming courses? He's right that setting up the needed software shouldn't be an impediment to completing work in a programming, but that's because the university should be preparing the students with those skills before they get to his course.
If you're going to need to configure a VM and toolchain for many of your subsequent courses, it makes sense to start off with a "configure a VM and toolchain" course.
Y'know, even at MIT 20 years ago, there wasn't an assumption that people knew how to use computers, even for the computer science classes. Each class had an evening lecture on getting through all the "bullshit" that you needed to get started and actually learn the interesting things, instead of the peculiarities of the latest flash-in-the-pan toolchain that didn't exist 5 years ago.
If you're going to need to configure a VM and toolchain for many of your subsequent courses, it makes sense to start off with a "configure a VM and toolchain" course.