Article 298 limitedly exempts Section 2. This makes sense because the purpose of UNCLOS is to settle maritime territoriality disputes.

See §§ 397 - 412 of the ruling [1] for the Tribunal's reasons Article 298 does not apply to many salient pieces of the Philippines' case, including those pertaining to "Scarborough Shoal" (§ 400), "Mischief Reef, Second Thomas Shoal, or Subi Reef" (§ 401) and others.

[1] http://www.pcacases.com/web/sendAttach/1506 page 140