"People prefer native apps to web apps" is talking about literally using an app on your desktop, in the dock, with keyboard shortcuts, rather than having a website in your browser. This is sort of shown by the amount of Electron apps people use — you could use slack, spotify, or vscode in the browser, but most people prefer to use the app.

"Java has UI curse" is referring to how when Java tries to imitate native UI (note the difference to "native app", which is in contrast to a web app), it fails and hits the uncanny valley. No-one likes it.

Given that, it's not a contradiction to have a native app, that does not try to use the native GUI toolkit of the host platform, using Skia directly to draw UI elements.