The second climbing entrance is the one my plane crashed nearby in my current save. It actually belongs to cave 1 (though the description is true, you'll find a lot of ropes, skulls and a fuel canister there - and bibles).
The missing entrance to cave 2/4 is in the middle of the clearing east of the yacht, west of the cannibal village, easy to spot if you make the yacht bay your home. https://theforestmap.com/#-18.6,1234.6