What I don't understand is where or what is my root directory? (i.e the instructions above),

var/www/html/store
Web Root or Store root???

If you have your shop at


var/www/html/store then your shop root is just that

If your shop is at the Web Root or var/www/html/ then that is the root of your shop

favicon.ico is at your web root or var/www/html/