The pensions are “underfunded”, indeed - and that means (surprise!) by legislation that taxpayers will be tapped to make up the shortfall.
Money is fungible, and what the CAFR documents is that (apparently) California is sitting on billions of dollars (outside of pension programs) that are not being counted.
While it has long been my wish to have a pony too, why shouldn’t the pension funds be tapped to pay off pensioners, versus raising taxes to exorbitant rates on others who have neither the means nor the inclination to fund these programs?
Pension funds are, in theory anyway, funds set aside to pay for present and future pensions. Raiding them to pay current general fund expenses is a really bad idea. Works for this year, but makes future problems much greater.
Similarly with most if not all of the other funds mentioned, I assume. The money might be there, but it is already committed by law to certain uses.
Now one might make a good case that some of these other uses are things the state shouldn’t be doing anyway, but I can guarantee you each of them has a rabid special interest group willing to go to the mattresses in its defense.