Is it possible to have one "WiX Installer" project in a solution in Visual Studio, but that one project outputs multiple installer files (either by having multiple .wxs files or multiple <Feature>s or however else)? Perhaps one .wxs file for one .msi file?
No. 1 .wixproj == 1 .msi, with the exception that you can have multiple localized versions of that one .msi.
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