menu Writer wasn't created to be aware of the Global Settings that are Created by site Sculptor if you select the option to use CMS, so yes it will overwrite the Local Root and Remote Root settings.
I will have this logged as a bug, it will need to be fixed in menu writer.
Really though, as long as the Site Settings for HTTP Address on the Local Info tab and URL Prefix on the testing server tab are configured properly, the change made by menu writer should not have any effect.
In your site definition, how have you set the HTTP Address on the Local Info tab?
What is the URL Prefix on the testing server tab?
In the database created by site sculptor, what is the value for the PCMS Remote Root record?
