I have the Microsoft Store version and as far as I can tell the only difference is that Cider pops up annoying "UPDATE NOW" dialogs when the update is posted here but hasn't yet cleared the Microsoft Store. So basically your updates are lagged a few days usually. That's all I think though.
Microsoft Store version is only available for Windows users. The itch.io version is available for Windows, Linux, and MacOS. If you only use a Windows PC, use the Microsoft Store version if it is much cheaper in your region. Updates pop-up doesn't interrupt my experience using the Cider App anyway (itch.io version).
