Learning a programming language has nothing to do with how it's seen by a computer. That's a different class (a class on compilers, maybe). You can even turn Java into Javascript if you want to[1]. The fact that the compilation/transpilation flow here is Java -> Java Bytecode -> JS is meaningless in the context of learning Java.
Learning the syntax of a progaming language might not have much to do with how it's seen by a computer but it's important if you want to learn how to use a language properly. If you don't know how Java(or any language) works fundamentally, the code you write may work, but it'll likely be more inefficient both in terms of program and programmer speed.
Debugging sessions will be more frustrating and take longer and generally the quality of the programs you write will be lower compared to programs written with a language's quirks and peculiarities taken into account. Which you learn by understanding how a language works.
I'm not saying they should be able to write a Java compiler or interpreter, but they should have a decent idea how they work at least fundamentally.
It's harder to learn this when it all happens at the push of a button and you never learn to appreciate that button because you've never had to do it yourself and if something goes wrong with that button for some reason, you won't understand how to fix it or work around it.
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.
The author, Leonora Tindall, is a woman.