CK,
Its all in the GSL gobs. You'll have to find the gob for the area containing the specific base and edit it with GSLedit. Then export the layer as a new gsl file. Assuming this will be part of a new addon campaign, the user applying your package would then install the gsl file with GSLman and this would wipe out all default objects pertaining to the stock base while simultaneously installing your new objects.
Read the PDF in the attached zip. You want to go directly to page 10 to get the info you need for the operation. The txt file contains a sample list of all of my installed airfields in my PTO setup - including stock - and their corresponding gobs. This should make your "search and destroy" mission a little easier. Once you identify the gob's code name, you can easier locate it in GSLedit's list. When you click on the gob in the list, you'll get a listing panel on the right which shows all the objects in that gob's area. Those items which have pictures in the INFO folder will display their images along with their dp file names. Those that don't will show as file names only.
Just keep in mind that you won't be able to manually delete anything with the program. It just gives you a listing of current items in the area. When you create your new gsl in MB, this will auto-exclude any stock items there, as the guide will tell you.