It’s funny and also a bit ironic. But from my experience we tend not to be able to apply advice for mistakes that we did not yet feel on our own.
At least that’s my experience. And the systemic and clean view on project structure can only really be learned once you are “forced” to use it. If there is no problem, the advice can not be applied. And when there is a problem, you can’t progress without it.
What I’m trying to say is that it will all come in time. You build Pong, you have new question. You seek new insights. You build something else and the (game) loop continues. And before you know it you love game development more than actually playing games. Well, at least that’s my experience :)