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This sounds like an application/website problem rather than an operating system problem. You don't need to distribute both an EXE and an MSI installer. That's like distributing both a .pkg installer and a .dmg/.zip for your Mac program. Just pick one technology. Most programs don't need both.

You don't need to use Microsoft's installer technology either. Installers are simple programs. You can roll your own or use third-party installer technology like NSIS. I remember old versions of Chromium had a very simple "installer" which was just a dialog that ran on first launch and asked you for some basic settings.

The architecture problem is easily solvable too. Simple programs can just target the lowest common denominator (32-bit x86.) You can simulate "fat binaries" by having a 32-bit x86 wrapper program that includes builds for other architectures as data, extracts the correct one to the Temp directory and runs it (I think Bvckup 2 does this.) For large programs, you can have an online installer which picks the right version and downloads it (with options on the website to download an offline installer.) Also, the website itself can point the user to the correct download. It doesn't even need JavaScript to do this, since the user's architecture will be in their user agent string. Use this information to emphasize the correct option in the UI. Maybe even hide the other options behind an "Other downloads" link.

You don't even need to bother with 32-bit x86. Nobody has 32-bit x86.

The ARM emulator only runs 32-bit x86 binaries.

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