I use over years CMake (now supports also C#, but you can use a bare Makefile to copy the required files and execute Wix commands) and Wix to create MSI install

I use over years CMake (now supports also C#, but you can use a bare Makefile to copy the required files and execute Wix commands) and Wix to create MSI installers automatically. Wix is IMHO the best option, if you want to create Windows-native experience. MSI installer format is the best one, especially in enterprise deployment, including AD networks. Additionally, signing the installers gives you additional value.