Most likely because you have dealt with them many times before that you don't notice them anymore or prevent them in the first place while setting up a project. But everytime I need to do something in Java I get bitten by this stuff, and I'm not the only one.
I've never had to, was my point. Not since waaay back in the day when I was first learning about it (more than 20 years ago). I came to java (commercially) 5 years ago, and it's not that I've dealt with it so much I don't see it, I've never had to deal with it.
Maybe things have got much better in the last handful of years, I don't know. My experience of getting started with a java project in that time has been no worse (and not really any better either) than in other languages.
Honestly I haven't had to deal with the issues you talk about in the last five years (which is as long as I've been writing java commercially, before that I was mostly a C developer).
Having had recent experience with Go and Javascript/Node, I can't say either struck me as especially easier or more intuitive to get started with.