In Windows there are further nuances, such as installing per-user, per-machine, or both. Similarly, MSI support often implies support for transforms (MST files) and patches (MSP files) also, which is important on large networks. Back in the days of constrained bandwidths, MSPs were great for rolling out updates without killing the WAN, but few vendors would provide them.
Firefox tended to prefer the interactive install wizard installers and hence deploying it at scale was an enormous pain in the arse.
For example, the Enterprise CA thing actually interacted with the packaging. You had to crack open the Firefox files, download some obscure NSS command-line tool that they regularly moved around on their website to spite admins, and inject your corporate certificates into the Firefox-specific Root CA file. After this, everything had to be put back together in some way for deployment, typically by repackaging the files into an MSI.
Similarly, instead of ADM Templates that allow settings to be pushed out via Group Policy, you had to do hideous things to JavaScript files. These also changed regularly and had all sorts of limitations.
There was just no way anyone in their right mind would do this every few weeks to keep up with the Firefox release schedule. IT admins have other things to do, not just babysitting Firefox, the one special and unique flower that refuses to play nice with Windows.
The only other obstinately anti-admin products I can think of that were this bad were the Java Runtime and the Adobe suite of products. Even Adobe provided an ADM template at least, even though they published it as a PDF.
Why was that important? I was under the impression that exe and msi installer had no real difference between them. Obviously I am incorrect but I am wondering why.