In the October 2019 release of Dynamics GP, when you build the check file, you have the option to include or exclude the additional withholding for Federal, State and Local tax amounts.  

By default, any existing build check default ID will have these settings automatically marked.  However, you can unmark the settings and save them with the build check default ID and they will be remembered in the future when you select that default ID.  

Now, you can do special check runs without having to manually update employees who have setup additional withholding amounts.