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I dont see what earthly difference an application uid could have on installing calibre portable, since the uid is specified at runtime, not install time.
As for what benefit accrues from having a fixed uid, you'd have to ask Microsoft, I am simply following their recommended best practices. Off the top of my head, I'd guess, it allows windows to recognize common applications and save whatever ui specific settings are saved by the shell for applications, like recently openend documents, window positions, monitor it was started on, etc, etc.
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