The difference between the two first principal components may be very small (as they are the two most important ones), but I guess it's right to say that the first one is bigger than the second one.
Mind that they are internally computed and you don't have access to the Eigen vectors, so it's a bit 'arbitrary' in a way. It's mostly a way to represent things in a user friendly way, and to let the user update the boundary manually (you can add and move the vertices boundaries in this 'plane').
And for the confidence, your interpretation of the meaning is right. For the exact way it is computed, I fear you'll have to dig into the Canupo article ;).
Daniel, CloudCompare admin