Installers that do not use MSI extract the installation resources from themselves and manage their own installation. Bootstrappers will contain an MSI instead of individual files. Installing the MSI is handled by Windows Installer when setup.exe is called.

From the Deploy Firefox with MSI installers Firefox for Enterprise article: (quote) Firefox Enterprise offers MSI installers per locale, per cpu architecture (32 and 64 bit) and per channel to help system administrators customize and deploy Firefox in their environments. The MSI installer (supported on Windows 7 and later versions) is a wrapper of the exe full installer that allows customizations through the use of a MST file prior to deploying through standard Windows deployment tools such as Active Directory or Microsoft System Center Configuration Manager.

More on offering MSI installers for Firefox downloads in this bugzilla report: Bug 1493205 - Expose MSI installers on mozilla.org for downloads _{See Bugzilla Etiquette before commenting in bug reports and other guidelines.}