Universal USB Installer doesn't simply extract files from an ISO and call it a day. It actually does the extras you mention, such as writing a proper MBR and aligning partitions so that your thumb drive will indeed boot the distro. Universal USB Installer is direct competition to UnetBootin and I tend to prefer the interface and experience of the former over the latter.
Also, you mention a "built-in" command that can make a drive bootable. As far as I'm aware, no such feature exists in a Windows environment when creating a bootable Linux thumb drive. Not to mention, dd for Windows is a third-party port of a UNIX application, which can be found on the Net.
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