The binary installer will of course overwrite the binaries (actually, I think they used to be wrapper scripts) in "/usr/bin/" and there is zero purpose in keeping the old lib/calibre. I'd just get rid of the repo version -- what do you need it for??
Just running the binary installer will unpack the binaries in /opt/ by default and then run /opt/calibre_postinstall which sets up /usr/bin/ and installs .desktop files and bash_completion scripts and other fun stuff. There is no significant time used up by this extra step.
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