I'm not sure what your experience is, but in the vast majority of enterprise AD forests, most apps are deployed by MSI and have been for quite a while. MSI actually took off really quickly, and most installer kits shrank a lot, many disappearing. These days most of the remaining large commercial installer kits generate MSIs as well as EXEs.
In my experience large Microsoft customers deployed applications with SCCM, now perhaps moving to Intune. Distributing MSIs via group policy is fairly primitive compared to what endpoint management platforms can offer.
But my point was that large commercial installer kits were always required to produce MSIs, in the absence of something like the WiX Toolset.
