Nicolas - Let's go with your method for a moment. Suppose from max rapid your machine takes 10mm to come to a controlled stop. You'd have to place your limit switch at least 10mm from where the machine absolutely must be stopped. Now suppose for whatever reason the machine finds itself heading for a position at 5mm from end stop. It'll hit the switch at 10mm and come to your controlled stop. Now suppose you go with the soft limit method. Your machine heads for the 5mm position, hits the soft limit at 10mm, slows down, gets to the 5mm position and CARRIES ON with the job. Which is better? Now suppose it's heading to a position beyond the end stop. It goes into the slow zone and then hits the hard limit - but it does this at a speed set to NOT damage the machine. It's win win either way.
Now your E-Stop - you get your arm caught - would you prefer it to stop NOW or let it chew your arm for another 10mm or so in order not to possibly damage the machine?
And now a confession - Many moons ago I used to think the same as you - that was until a younger Hood and others put me right