So, I find their description unnecessarily confusing. Basically, you are free to define any scale factors you want for voltage, current and impedance. You define it, or they define it. In this case, they defined it.
In the first part, you said you understand that the factor of 1000 is used to convert MVA to KVA. This is certainly true, but what they don't make clear is that they chose to use the factor of 1000, and it was not a necessity to have a factor of 1000 there. That is a very important point to understand. Once you understand that, then the impedance case should make sense. Whatever they wrote is correct because they decided to define it that way. There is no need to figure out why that value is correct because you are free to use another value if you choose.
Having said that, you do want your choices to be logical and intuitive so that you don't get confused by your own choice of unit scaling. Hence, you can see the logic in their choices if you look at them carefully.