This is as I suspected, and why I was not worried.
There are a few things that are "hardcoded" using a url like ~/root/store/product
If I change those to ~/store/product and then change the IIS set up then I should be good to go right?
I try and let the system dictate the URLs to avoid things like this, but when I do need to "hardcode" a URL how do I do it correctly?