Any idea what those situations are? I'm assuming that the TMS would make the decision?
Not unless the TMS is competent in the relevant rules, and has the necessary route knowledge to know if there's a tunnel up ahead, or a station, or....
It's down to the driver to make the call as to whether to override the brake demand, although the train must brought to an immediate stand if a passcomm is operated as the train is leaving a station, or if there is an immediate danger.
On some newer traction the brake demand cannot be overridden if the speed hasn't exceeded a certain level since the last door release and dispatch, this being on the basis that this is likely to be because the train is leaving a station.
I was on a GWR 800 (possibly 802) the other day and the 'emergency handle' was labeled something like 'communicate with the driver in an emergency' nothing about it being an emergency stop. Has the whole 'pull the cord' procedure changed on modern classes or just the labelling?
Some of what are labelled emergency alarm on an 800 are call for aids which don't apply the brake.