Finding permutation polynomials with low differential and boomerang uniformityis an important topic in S-box designs of many block ciphers. For example, AES chooses the inverse function as its S-box, which is differentially 4-uniform and boomerang 6-uniform. Also there has been considerable research on many non-quadratic permutations which are obtained by modifying certain set of points from the inverse function. In this paper, we give a novel approach that shows that plenty of existing modifications of the inverse function are in fact affine equivalent to permutations of low Carlitz rank and those modifications cannot be APN (almost perfect nonlinear) unless the Carlitz rank is very large. Using nice properties of the permutations of Carlitz form, we present the complete list of permutations of Carlitz rank 3 having the boomerang uniformity six, and also give the complete classification of the differential uniformity of permutations of Carlitz rank 3. We also provide, up to affine equivalence, all the involutory permutations of Carlitz rank 3 having the boomerang uniformity six.