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NSIS installers can be wrapped in MSI files using the MSI Wrapper. It is a small tool that I made for wrapping NSIS and Inno Setup installers. It uses WiX to compile the MSI but there is a GUI to help you instead of an XML file.
It was made because I needed a tool for creating MSI files based on traditional EXE installers. I needed support for uninstall and upgrades and only wanted the wrapped installers to show up once in the Add/Remove programs in the control panel.
I also wanted to be able to pass command line parameters to the wrapped installer when the MSI is installed.
If you want to use it or help me improve it, you can find it at http://www.exemsi.com.
I share the opinion that wrapping an executable installer in an MSI package is not the ideal solution. However, when you already have the exe it can make a lot of sense :-)