I use an IntelliJ IDE and open folders all the time and it's never created any cruft to clean up. I think that only shows up if you start making project configurations (like file watchers to run preprocessors for web languages)
It still makes a .idea folder to add to .gitignore or clean up, just as .vscode makes a .vscode folder.
I don't see this as a lot different than MacOS spraying .DS_STORE files everywhere. It's not a big deal to add to .gitignore, but it does leave a fingerprint. It's just that tries to determine reasonable defaults if the path doesn't exist instead of Netbeans/Eclipse/whatever forcing you to pick them with a wizard if you want any of the "real" features to work.
