Folders in Applications not in sync with Launchpad
Solution 1:
The two hierarchies are separate, and cannot be kept in sync without third-party intervention. Even then, there would be difficulties. Note that Launchpad folders have capacity limits that actual folders do not have, and folders within /Applications can contain nested folders, while Launchpad folders cannot.
It's just a coincidence that the apps in /Applications/Utilities match up with the Utilities folder in Launchpad. On my machine, I moved Terminal out of the Utilities folder in Launchpad, but it's still /Applications/Utilities/Terminal.app