Of course, the crucial assumption here is that it is possible for humans to acquire a set of reasoning skills so thoroughly and reliably that they will actually apply them to all issues, no matter what. I don't think this is possible, and with this in mind, I still don't think the "waterline" concept is useful.

Keep in mind that this concept was introduced in the context of teaching others. The practical advice is to teach skills that will enable people to give up their false beliefs rather than directly arguing against the false beliefs, both because emotional attachment makes a direct attack more difficult, and because the particular false beliefs you observe are indicators of a larger problem. This does not require the most extreme case that the person will universally apply the skill in all situations no matter what, though the more reliably the person uses the skill, the better it works. If using a set of skill 90% of the time makes a upperbound of 10% probability of making any instance from a class of mistakes, that is not as good as using the skill all the time and never making that kind of mistake, but it is still useful.

If anything, it's dangerous because people may fall into the trap of thinking that they are above a certain waterline, whereas in reality, there are issues where due to all kinds of biases, even the very basic skills are failing them.

Again, this is a technique for teaching. Don't use it as an excuse to trust yourself.