Julia was trying to comment on this post, but neither she nor I could make the comment go through, so I'm putting it here as a separate post:
Technically, the accession protocol should be an independent legal instrument that establishes China's accession to the WTO Agreement, which means it should be separate from and outside the WTO Agreement itself. However, the accession protocol declares itself to be "an integral part" of the WTO Agreement, thereby making itself part of a covered agreement under DSU. Note that this integration is also the legal basis for subjecting the protocol to the WTO dispute settlement mechanism, since the protocol does not otherwise say so explicitly.
Accession to international organizations or treaties is normally done through a legal instrument that does not contain substantive obligations. Consequently, there is no issue of coherence between the provisions in the accession instrument and the provisions in the underlying treaty. The WTO accession is unique. When you have an accession instrument that sets out numerous substantive conditions for accession, and at the same time declares all these conditions are "an integral part" of the underlying treaty, you are bound to be thrown into a strange situation for treaty interpretation.
Facing this unfortunate reality, the WTO treaty interpreter has a policy choice to make - treat the protocol provisions and all the relevant WTO provisions on the same subject matter in an organic or holistic way unless the protocol explicitly says otherwise, or treat each protocol provision as independent from the underlying WTO agreements unless the protocol explicitly says otherwise. So far the AB has chosen the latter approach - a strict textualist approach that is. I guess it is politically safer to do so, given the fragile state of affairs at the WTO.
As for the relationship between GATT XX and other WTO agreements, the most critical test would be to the SCM. Subsidy issues are one of the most difficult issues to tackle conceptually, especially after the global financial crisis.
For those who are interested, I have explored the challenge involved in the interpretation of the accession protocol, including one published in JWT Vol. 44:1 (Feb. 2010), and one in Chinese J. Int'l L. Vol. 10:2 (Jun 2011). The pre-publication versions are available at http://papers.ssrn.com/sol3/cf_dev/AbsByAuth.cfm?per_id=625173