HyperSizer calculates the Tsai-Wu criteria at the inner and outer surface of every ply and the margin that is reported is the minimum margin for any ply, for any component. So it doesn’t have to make a decision about what is the “highest” stress because for each interactive failure mode, the interactions between the stress components are different. Hopefully, this explanation doesn’t overcomplicate it for you.
The short answer to your question is yes.
Phil