I just talked to the technical manager at one registrar today - AQSR. Basically if your scope of accrediation is 100% automotive, you will receive one certificate for both ISO 9001: 2000 and ISO/TS 16949: 2002. If scope is only partially automotive, you will receive one TS certificate for the automotive scope and one ISO certificate for the non automotive.
So, if 100% of your business is making car seats, you get one certificate for both.
If 50% of your business is making car seats and 50% is raising tropical fish (not used in cars), you get a TS certificate for making car seats and a ISO certificate for making seats and fish.
This may just be one registrars policy. Not sure if they all follow it.
Tom