In an amicus brief in the Canada - Renewable Energy case (DS412), several NGOs make the argument for GATT Article XX to be treated as an exception to the SCM Agreement. Here's an excerpt:
1.3 The reference to ‘this Agreement’ in Article XX does not foreclose its applicability to the SCM Agreement
The term ‘this Agreement’ in the chapeau of Article XX of the GATT 1994 has no clear ‘ordinary’ meaning of its own. This term was contained in the GATT 1947, prior to the Uruguay Round, when the GATT 1947 itself constituted the primary multilateral trade agreement. The GATT 1947 was carried over into the WTO Agreement essentially as it is, without being rewritten to take into account its new place as one of many related ‘goods’ agreements, bound together in an annex. The reference to ‘this Agreement’ must, therefore, necessarily be interpreted in the light of today’s placement of this provision and the link of the GATT 1994 to other Annex 1A agreements, as discussed above.
In China – Audiovisuals, the Appellate Body did not interpret the reference to ‘this Agreement’ as limiting the application of Article XX to the GATT 1994. In the earlier Brazil — Desiccated Coconut case, the Appellate Body found that the meaning of ‘this Agreement’ in Article 32.3 of the SCM Agreement refers to the SCM Agreement and Article VI of the GATT 1994. Accordingly, the meaning of ‘this Agreement’ is not inherently limited to the covered agreement that it is used in.