" but we will probably see what the USSC has to say about it."
Actually, we will probably not. They almost certainly will not take the case. This is a matter of state constitutional law, and well settled law at that. The big problem for Khosla is: It's been that way since 1976, and the supreme court has not, in that time period, said there was anything wrong with the provision.
This is part of the California constitution:
"No individual, partnership, or corporation, claiming or possessing the frontage of tidal lands of a harbor, bay, inlet, estuary, or other navigable water in this State, shall be permitted to exclude the right of way to such water whenever it is required for any public purpose, nor to destroy or obstruct free navigation of such water; and the Legislature shall enact such laws as will give the most liberal construction to this provision so that access to the navigable water of this State shall always be attainable for the people thereof." - California Constitution, Article X, section 4
At worst, they will be forced to pay market rate.
They will then argue over market rate.
Khosla may be a billionaire, but bureaucracy generally doesn't care.