You have completely missed the author's point. The issue is not "how can we help students learn to code" the issue is "how can we help students understand the systems that they are coding on since that affects how they code"

Knowing Java runs in a VM very much affects how you have to code. Sure, when you are learning in a 100/200 level class it doesn't, but by the time you graduate if you don't understand the implications, that is bad. Why not make a very simple change early on that gives context for students later on? We shouldn't be teaching students that Java runs in a virtual machine in a 200/300 level class, by that time we should have moved on to why that matters.

Forcing students to continually use java/javac will make them start learning the concepts on how a computer actually processes their program. It makes them think a bit more about it and the concepts are not foreign when they learn it in a full class. The IDE just turns the whole process into a single button with little context.