Hello. I want to install InkScape on my virgin 64-bit Windows 10 machine as cleanly as possible (so that if needed I can cleanly uninstall it). What is the difference between the Installer (msi) and the binary archive?

I also see for 32-bit Windows there is a portable app. What is that?

That sounds like "mission impossible" to me.

But I think the portable version is meant to be used on a flash drive or similar. Maybe that's your answer?

Normally, the portable app would be the "cleanest" install, I think, meaning that all related files will be confined to 1 directory of your choice. To "uninstall", you would simply need to remove the directory. See Portable apps support:

Delete the AppNamePortable folder to completely remove the app and all its settings.

Anyway, I don't think Inkscape messes a lot with your system, and personally I would consider a normal install and uninstall clean enough. But that's for everyone to decide, of course.