When you run zc_install it will set the SHOP to shop if that's what you enter in the fields where it asks you those questions during zc_install.

And zc_install does its thing regardless of whether you're on linux or windows.
Your problem is NOT with linux. Your problem is that your new server has a different folder/path structure, and your existing configure.php files don't contain the correct information. Running through zc_install will populate those files with the correct information for your new server. THAT is why that's part of the instructions in that article.

Follow the instructions first. Then if there are further questions, feel free to ask.