Has also happened to me for certain military tents north of NW:AF
Ground geometry set too high?

simply crouching fixes this though, so its not a major bug.

Absolutely, however, the foundation is laid. It isn't a broken system, but it just requires some tweaks. I'm grateful for the new notifications that inform you when you are hungry, thirsty, healthy, etc

This is simply ignorance of the new system.
you need to drink and eat until you get a notification like "you are feeling full."
When you spawn, you are incredibly low on health (ie, very thirsty and hungry).
Therefore, you will quickly begin seeing "I am thirsty" notification. When you drink, you only recover from critically low health, but your stomach still isn't full.
Liken this to a car that's near empty on gas. You can put a gallon of gasoline in it, and that puts it right above E, but it doesn't fill the tank, and eventually the car will approach empty again.
This is why you see constant status updates, because you are hovering around critically low health. you may drink to stop the notifications, but you do not fill your stomach.

lrn2 realism.

This happened to me when I reached critically low levels on food and drink.
status messages were like "my head throbs" "I need to drink" [in red] etc

But then I ate and drank until I got a message like "I feel full." I haven't seen a single status since (I hope its because I am playing it right by resting often and eating and drinking whenever I can). But my screen is still desaturated.

The blurryness can be fixed by simply opening to the Video Graphics options. You don't need to tweak anything - just by opening the video options the blurryness goes away. But the screen is still desaturated.

what are rods and cones

To expand on the idea that if you see a status message you are only 25% full - if you drink or eat there should be an indicator that says something like "Your thirst was quenched - but you still are not full" or something like that. To let the player know that even though they have recovered from CRITICAL condition, they are still not at FULL health.

I have played with one character for 12 hours now. I no longer see any status messages at all. I keep well-fed and drink and rest often. Initially I saw these messages all the time, and I nearly died of thirst/starvation. But then I found a water source and I ate and drank until there was a message like "You are feeling full."
I think your character needs babying in the initial stages. You can't just sprint everywhere (in fact, I rarely sprint), you need to take rests quite often, and you need to eat and drink. But then, he will toughen up. I think new spawns need an acclimation period.

The only real bug is that, even after I have supposedly recovered from my near-death experience, my screen is still desaturated and blurry, but can be fixed by simply opening the Video/graphics options (I don't even need to touch anything. just open the menu)