If you look in the zip, you will see that it mirrors the structure of your Rom. Inside the zip, is a system/app folder. Within it are .apk files. Apps.
Basically when you flash the zip, everything in the system/app folder is put in the same place on your Rom.
So of you took all the apks out of the zip, you could put apps in there yourself, to flash.
Benefits are you don't lose internal memory space with these apps.
But, system apps can't be updated via the market.
Use quick system info to see how much system space you have available.