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Well, it turns out building a calibre-0.9.10 .deb package was as easy as uscan / uupdate. I will test it and upload it to my PPA.
I don't keep unused packages. But I *prefer* to keep my USED packages in the apt database (as opposed to informally-managed manual installations). Package managers like dpkg and rpm where invented for a good reason (and apt and yum for *another* good reason).
As to the option of having both a manually-installed and an apt-installed package (with different versions): that can lead to problems, because it's unclear how programs locate shared libraries / configuration files / dependent binaries. You never know which version ends up taking precedence.
Perhaps the above may not apply for calibre, but I've had nasty experiences with other packages (e.g. jack)
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