Look, I was being a bit snarky. I think all apps that are not native, or don't follow system convention, create an impedance in that they don't always follow system conventions, or something about them doesn't work exactly as it would in a native app. This can cause confusion in users. The level of impedance depends on the user skill, experience and expectations. I know traditionally, Mac users have cared a lot about consistency and following the HIG, whereas Linux users are more likely to pick the application they prefer and not care whether it is GTK or QT.
If you are someone who jumps between Windows, Linux and macOS using the same app then consistency in how the app works is a big gain for you, and then the impedance comes from the system you are using.
I didn't mean to imply that Java apps are bad, far from it. Many java apps are good, they just stick out like the proverbial, and performance historically was not as good as native apps. There was a time when the go to torrent application was java based and Netbeans and Eclipse were the IDEs of choice. But they made trade-offs, and two of the key ones are performance and consistent UX with the operating system. For many applications / users, this is a fine trade off to make. But Atom made a similar trade off and then the developers have spent all this time and effort trying to improve performance, and that is what I was trying to be snarky at, that its obvious why performance will always lag.
