The Apple developer ID is in no way linked to the app store consumer ID.
The app store account you use to download the latest release version of Xcode 4.3 + will only be required to update said Xcode.
When using Xcode you might need to use your Apple developer ID (free) to download additional resources (documentation, support for anterior iOS versions/SDKs, command line tools)...
You can register for an Apple developer ID here for free.
To submit apps you need your Apple developer ID, which you will use to register to the Developer Programs:
- Mac Developer Program ($99/year) for distribution on the Mac App Store
- iOS Developer Program ($99/year) to distribute your apps on the iOS App Store.
These programs will also give you access to additional resources and beta versions of OS X, iOS, tools and SDKs. For beta versions of Xcode and beta frameworks you need to use you apple developer ID to download the DMG with the beta version directly from the developers portal.