It's not really a problem it's intentional. Most of the people who use the Installer don't have root passwords setup because they don't have a good enough working knowledge of MySQL to do so (if they did they wouldn't need the installer, now would they?) My belief was and still is having an extra password prompt could lead to noobs becoming confused and the whole point of the installer is to avoid that.
More advanced users who setup a root password or who would just like to do everything themselves may download the raw pack, same software just no installer.
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