Solved it myself after reading the CPP code for the portable executable! (
here)
It just needed to set an environmental variable first.
Here's a snippet from my final batch file.
Code:
SET "CALIBRE_CONFIG_DIRECTORY=G:\path\to\portable\calibre\Calibre Settings"
G:\path\to\portable\calibre\Calibre\calibre-customize.exe -a helloworld.zip
G:\path\to\portable\calibre\calibre-portable.exe