Typically Windows applications bundle all their dependencies, so Chocolatey, WinGet and Scoop are all more like installing a Flatpak or AppImage than a package from a distro’s system package manager. They’re all listed in one place, yes, but so’s everything on FlatHub.
That’s more likely to be the tool assuming it’s running on a case-insensitive filesystem than it is Windows breaking anything. If you mount networked storage running on a case-sensitive machine, that’s something that’s worked fine in Windows for a very long time.