Both BART and Muni had problems with the service brakes on their new trains flat spotting the wheels – apparently it's still not quite as much a solved problem as it should be. BART especially tends to run their trains with out of round wheels – almost certainly not helped by running aluminum wheels.

Exactly. After initial testing of the rubber tires in the 70ies, RATP quickly decided to not use the full acceleration/breaking potential of the rubber tires, because it was very uncomfortable for passengers.

True, though emergency braking isn't entirely subject to these limitations.

At least for tramways I know for sure[1] that the tram will happily have you break your arm inside the tram because it braked too strong in case of emergency rather than crushing a pedestrian that crossed in front without paying attention.

Maybe the rules are different for metros though, given that there aren't as many pedestrian on the way…

[1] because I got the information from the system design team of a big tramway manufacturer I worked with no later than last year so my memory is much fresher, and the source is more reliable.