Browser preferences (now under the Console > Jadeite menu) allow you to hide Package Groups (good). You can also hide Packages. When you do this, it leaves a large empty pane in the browser. It also makes the browser unusable since you don't see any classes if you don't have a package selected.
If you do want to hide the package list, it should automatically present all classes in all the packages, so you can work with those classes.
For the first release, we can just leave as-is. The ugly hole makes it obvious that something isn't fully tested and intended to work, so when it doesn't work you are not surprised. While avoiding thinking about packages might be nice, it's not essential... and might be risky in practice.