Reading the article, it's clear the reason is the state froze the budget in 1982 and left it that way for 40 years. As with everything else in California, they could have done something about it, and didn't.
I'm sure the reason they froze the budget, though, is because they couldn't fund it further. Whether or not the lack of growth in funding is due to Prop 13 is not something I care to figure out or verify, but it sounds plausible.
The article also states that the growth of the fund is legally limited to cost of living increases.
Since this is a state wide law for a state defined budget, the solution is simple: repeal the law (which they did in 2022) and allocate funds to it from a different program, or with a new tax, such as a sales or income tax increase.
This is how they do a lot of things. I seem to recall at one point a rep wanted to add a tax to blueberries so they could create a blueberry commission to advertise California blueberries in other states. I think they do this already for other crops like avocados, though I'm not sure if it ever actually became a thing.
In any case, all of the legal levers have existed to fix the problem. They simply chose not to.
