Having similar issues, activating the trainer causes crashes to desktop when doing things like fast-traveling to a location that is one district or more away - weirdly seems to work when fast-traveling to areas local to the district you are in.
Have also raised an update request.
I just tested the game and used all of the fast travel locations available to me and it works fine. I would suggest verifying/re-installing the game
I made an update request as I cannot seem to make the freeze challenge timer to work in the DLC's like Catwoman for example. Sceewball's challenge timers do not stop
I made to separate timer options already. It may be that there is 1 more, 10 more, or a separate function for EVERY timer in the game. With that said, the game is a time sink if I were to try and go to each one and then make a separate option for each. I don't think saves are shareable either, so I would have to buy this DLC, then play the game hoping at some point, maybe in hours, that I get to that location and challenge, then hope I could actually make an option for it.
It may be that I am not going to do this, as there is a limit to how much time we can spend on a title with that many functions (possibly) that would individually need to be accessed for EACH timer.
best,
Cal