Most of the time, it has to do with how they are speaking. Men usually speak from deeper, in the chest. Whereas women tend to speak from higher up, from the mouth or nose area. When MTFs train their voice, they focus on training it to speak from a different place. With FTM, our vocal chords will stretch and change and resonate differently on T because of how T changes us. However, some FTM naturally speak from higher up and that could be part of the reason some voices still sound a different pitch. That can be changed with training, of course, and it can also be a combination of other things like pronunciation or emphasis. A way of speaking is something we acquire socially so it affects different people to different degrees. some Cis men speak from higher up naturally and some cis women speak from their chests. That is one thing someone could focus on trying to train, though, to have a deeper, more resonant voice. There are videos and tutorials that might help if that's something of interest.