you hit the nail on the head. MSIs support two very useful features: transforms and Installs via GPOs. This makes customizing the install of the launchers and installing them on a large number of machines very easy for enterprise deployments. for example:
Transforms: you can add shortcuts which are advertised and self-healing (if someone uninstalls the launcher it will re-install when a user clicks on the shortcut). This can also bundle a configuration json and drop it within the launchers install dir making it a Pre-Deploy install. This does have some caveats with permissions and users modifying the configuration obviously though.
GPOs: Domains can use GPOs to install the launchers, configuration JSONs on a per-user basis, and pushing trusted root certificates which couple with the trust.store launcher property to use the system trust stores.
Both of these methodologies require a bit more knowledge around windows administration, but those that are familiar with it these new MSI installers make using the launchers in their setups much easier to work with.
Hope that gives a bit of info!
Jonathan C