There are about 20 tools that build MSI files, and some of them let you customize the UI sequence and add your own dialogs, fire custom actions off their buttons and so on. InstallShield is probably the best known of the companies that build MSI setups. You're probably assuming that the SQL Server Setup project is built with a Visual Studio setup project, but they are somewhat limited in feature content and probably weren't used.
You can do your project both ways, as was mentioned. Start with a web setup project and then make a custom folder corresponding to TARGETDIR for the other files, or start with a setup project and install the web site with custom actions. It's hard to predict which works best for you because it depends what the rest of your setup is doing, but the web project and adding a custom folder lets you take advantage of the web setup installing the virtual directory and the web site.
Or you can use one of the other tools from InstallShield, Wise, Advanced Installer, or Wix or something to build a setup file, but just keep in mind that Visual Studio setup projects are not the only way to build MSI files.
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