WinMerge's Compare As > Disassemble IL Code and Disassemble Native Code options appear to be almost completely undocumented, so when I came across the error message Visual Studio not installed
I wasn't able to find any relevant information online. I'm hoping this document will help anyone who runs into the same problem in the future.
If you don't care about the explanation, you should be able to solve the problem by opening the Visual Studio "Developer Command Prompt" and running this:
mkdir "%APPDATA%\WinMerge\Commands\ildasm" "%APPDATA%\WinMerge\Commands\dumpbin"
where.exe ildasm.exe >"%APPDATA%\WinMerge\Commands\ildasm\ildasm.txt"
where.exe dumpbin.exe >"%APPDATA%\WinMerge\Commands\dumpbin\dumpbinpath.txt"