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.
I suspect the biggest issue here is that whoever sold him the property talked those lands right up as a selling point and he's discovering the reality is more complicated
I suspect he has lawyers to deal with that sort of thing. Do you really think he spent nearly $40 million based on what the seller told him about a treaty without checking with a lawyer?
It's not clear to me if he understands that the current court case is invoking federal supremacy of US treaties over California law/constitution, which seems to be a brand-new argument. He compares it to a private homeowners association barring access to waterfront, which to me seems completely irrelevant.