If both iPod Updater 2004-04-28 and iPod Updater 2004-07-15 are in your Utilities folder, iTunes 4.6 opens iPod Updater 2004-04-28.
You can use this updater if you want. The two are essentially the same. iPod Updater 2004-07-15 only includes support for the iPod (Click Wheel). Earlier iPod models, including iPod mini, can use either updater.