Writing settings to the traditional application directory is actually frowned upon on Windows. So unless you're willing to educate your user base on how to install a program completely within their own userspace (something the vast number of Windows users have no interest in learning), the traditional Program Files directory is the best way to provide a hands-off installer for the users who have no need or want to investigate, choose, and implement what amounts to a third-party Windows software repository. Having the program's settings, preferences and add-ons write/install to AppData provides a way for users to maintain their settings across updates and even uninstalls. Remove a portable app's directory and all settings, preferences and addons are gone. If they're not, then they can't really claim portability, no can they?
The only registry entries Sigil makes on Windows are the uninstall entry (Add/Remove Programs) and the optional installation choice of whether or not to register Sigil as the default handler for .epub files.
Other than that: one program folder, one settings/preference/addons folder for Sigil on Windows. I don't think that's excessive.
The bottom line is that large-scale portability and third-party software repositories are a pipe-dream on Windows for all but the tweakers and fiddlers. Always will be. And Sigil already provides mechanisms for those same tweakers and fiddlers to take control of Sigil's installation/configuration through environment variables if they want.
So much like I'm not interesting in catering to FlatPak or AppImage on Linux, or homebrew on Apple, I'm not interested in catering to Chocolatey, PortableApps, or SyMenu on Windows. They have their work, and I have mine.
Happy to accept a pull request for a portable Windows solution that supports all of Sigil's current features (including bundled python and plugin framework) that doesn't interfere with the traditional install/update experience the vast amount of Windows users expect, and doesn't require me to maintain/update xml files that are not required for building/installing Sigil on Windows.
I'm not mad or offended, I'm just not interested. So this will likely be my final post on the subject.