100% with you on the "we can't just pretend like people weren't living here just because they weren't white" BUT, from your article:
"Prior to European contact, California Indians had 500 distinct sub-tribes or groups, each consisting of 50 to 500 individual members."
Assuming that all 500 tribes were 500 people, that's only 250,000 people. Relative to the geographic size of the state, that's a pretty low population density. And many of the the areas of large growth wouldn't have been useful to a pre-industrial civilization, since they required so much labor and technology to exist (like say, pumping in water from 4 neighboring states in order to meet the needs of the population).
Let's settle on "It had a relatively low population of Indigenous people to area" instead of "it was empty", and call it a day?