The Apple developer ID is in no way linked to the app store consumer ID.
The 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 to download additional resources (documentation, support for anterior iOS versions)... You can register here for free.
To submit apps to the app store you need an Apple developer ID and you have to register to the Mac Developer Program ($99/year) and/or the iOS Developer Program ($99/year) to be able to distribute your apps on the Mac App Store and the App Store respectively.
These programs give you access to beta versions and other resources. 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.