According to the apparently well-informed first comment[1] on that article, it's not really an exception. The first paragraph:
As a former Coastal Commission staff member in the 1980s,
I've seen this scenario played out over and over. The so-called
issue of Spanish land grants pre-existing and somehow
superceding laws like the Coastal Act isn't an issue at
all -- land grants occurred in the early 1800s all over
California, so Martins Beach isn't any special or privileged
circumstance.