The modern installer packaging format for Windows these days is MSIX. From what I’ve read, if Avogadro works as an MSIX, that should be the preferred choice. It apparently provides a pretty easy UX for both users and devs.
Programs packaged as an MSIX then install via the system App Installer, it’s easy to put them onto the MS Store, and they can be distributed via WinGet as well (I believe WinGet requires apps to be an MSIX).
The official documentation has a bunch of info. It seems it’s possible to repackage an existing installer, though they recommend doing it from source code. Tools for creating them are built into Visual Studio, or it can be done from the command line.
Windows apps installed in this way run in containers, so like when creating the Flatpak, there might be one or two things (e.g. network access, plugin downloads) that need careful configuration. I believe this would mean that a Python interpreter/Pixi would have to be included in the app bundle for the interprocess communication to be allowed. See this page for restrictions.
For MSIX applications must also be able to install without user interaction so that they can be installed e.g. in an automated fashion or via the one-click install button in the MS Store. So I guess user choices for things like whether to install Pixi wouldn’t be obtainable, and the bundle would have to look more like the Mac/Linux bundles.