This setting disables the explorer jumping:

  "explorer.autoReveal": false

And here are some settings you can play with to get that window/instance behaviour under control (default values shown here):

  "window.openFilesInNewWindow": "off",
  "window.openFoldersInNewWindow": "default",
  "window.openWithoutArgumentsInNewWindow": "off",
  "window.restoreWindows": "all",
  "security.workspace.trust.untrustedFiles": "prompt"