The JVM is a virtual machine, just like V8, and neither is particularly "native." Java is an easier-to-optimize language than JavaScript, mainly because static types give better information to the compiler and prevent certain kinds of hard-to-optimize behavior from being written in the first place.

That being said, as someone who's used both Atom and IntelliJ a fair amount (although my daily driver is Vim), you can definitely see the downsides of using the JVM vs V8 in terms of startup cost. People complain about Atom being slow to start, but IntelliJ is so, so much worse — elsewhere in this thread dstaley mentioned it being almost 4x worse on a test file, and in large projects I've seen IntelliJ take literally minutes to begin being usable. The JVM is optimized for long-running server processes that can afford time to boot and warm up; the V8 team spends inordinate amounts of time ensuring that JS can begin executing quickly, even sometimes at the cost of peak performance. And RAM usage in IntelliJ isn't pretty either.

I don't think using the JVM instead of Electron buys much (if anything) in terms of editor performance compared to writing in native languages, like Rust or C++, and using native GUI toolkits instead of Swing/JavaFX or the DOM.