I spent the majority of yesterday playing with
AutoIt scripts, having it download the latest installer file, check to see if an install already exists and if it does, update it (moving the 'Calibre' folder to a back-up location first). During the update process, my script automatically closes the 2 pop-up dialogue windows - the 'Confirm update' as previously detailed above and the 'Success' dialogue. It's a bit messy but it works for me.
I now need to adapt my script for your changes. Now if you could just lose that 'Success' dialogue box as well, I wouldn't need my script at all

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For those wondering how Kovid's new option kicks in, you must specify an install path when running the portable install file e.g.
calibre-portable-installer.exe "C:\Calibre Portable"