Just a heads up, something about the way this mod changes the station names causes Shuttle Trains to eat itself upon opening it's GUI. As soon as any dynamic stop has it's name changed, you can no longer use shuttle trains in that save without toggling shuttle trains off, loading/re-saving the save (and wiping the shuttle data), and re-enabling it (assuming you also remove or stop using this mod, or it will just break again). This will of course mean you loose any existing shuttles.

Does renaming a stop manually break shuttle train? If so, it's probably their bug.

While I agree it is their bug and not Dynamic Stop's (not pointing fingers for blame, just a PSA), renaming a station manually does not cause the error.
Only changing a stop via dynamic stops causes the error. I suspect it has something to do with the way the dynamic control stop gets removed and replaced; shuttle trains is undoubtedly storing all stops in an array (so it can build it's gui) that only gets updated via methods that player or biter actions would trigger, but this mod bypasses. This causes Shuttle Trains to blindly attempt to access data from an entity that no longer exists.

Ultimately, shuttle trains should have a sanity check in it to make sure entities still exist before attempting to read data from them.

You are right, Shuttle train needed that sanity check, and that has now been implemented, so there is hopefully not any compatibility problems now.

Shuttle train crashes once more

Dynamic Train Stop v0.1.2 / Shuttle Train v1.1.2

It also seems to break FAT controller v0.4.19