In index notation it makes sense as
$$\sum_j {A_{ij} A_{jk}^T} = \sum_j {A_{ij} A_{kj}}$$
But this doesn't make sense for Einstein notation where in
$$A^\mu_\sigma (A^\sigma_\nu)^T = A^\mu_\sigma A^\nu_\sigma $$
and the sum is taken over both covariant indices, which is incorrect.
Also how do you know when to include a transpose when going from Einstein notation to matrix notation? For example:
$$\Lambda^\mu_\sigma \eta_{\mu\nu} \Lambda^\nu_\rho = \Lambda^T \eta \Lambda$$
How do you know that one of the lambdas is transposed?
Follow this hint: $$(AA^{\top})^i{}_j=A^i{}_s(A^{\top})^s{}_j$$ $$\qquad =A^i{}_s\ A^j{}_s$$
You can verify for with $$ \left[\begin{array}{cc} A^1{}_1&A^1{}_2\\ A^2{}_1&A^2{}_2 \end{array}\right] \left[\begin{array}{cc} A^1{}_1&A^2{}_1\\ A^1{}_2&A^2{}_2 \end{array}\right]= \left[\begin{array}{cc} A^1{}_1A^1{}_1+A^1{}_2A^1{}_2&A^1{}_1A^2{}_1+A^1{}_2A^2{}_2\\ A^2{}_1A^1{}_1+A^2{}_2A^1{}_2&A^2{}_1A^2{}_1+A^2{}_2A^2{}_2 \end{array}\right]$$