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I run Calibre directly from source, as do many others. I also control which programs can access the Internet and which can't.
Kovid tells his users exactly what info he sends and keeps. Given the effort he has put into Calibre, it's not unreasonable for him to track how many unique users he has, and I let Calibre communicate freely. It's on e of the few programs I actually trust completely.
You are free to block communication with his servers, or to read the code you are running or to modify it so it doesn't send anything. Kovid has made it amazingly easy for users to run directly from code instead of the compiled binary. If you want to compile from scratch, you are free to do that, too. I don't know what more anyone could want.
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