Even so it only matters once you try to run calibre. The existential status of the binaries will not edit the configuration data, that happens when you run calibre. I agree it cannot hurt to make sure to run calibre with each new weekly snapshot, but merely installing them one after the other does nothing. Nor does moving from an old version to the latest, if you don't run calibre.exe
The MSI will not touch the appdata. It is an easy experiment.
