Store the libraries inside the Calibre Portable folder instead of root (or elsewhere) so calibre-portable.exe can automatically map paths. I tried it with drive at G: and even when the status bar says D: when mousing over, it successfully opened my other libraries. It even remembers the last library opened.
Code:
\Calibre Portable
\Calibre
\Calibre Library
\Calibre Settings
\Other Library 1
\Other Library 2