That I do not get, whenever I have wired up roller shutters or similar equipment that has upper and lower limit switches I have always wired up the upper and lower switches in series with the E-Stop via a N/O (no-volt) contactor so if any of the three are operated the contactor coil loses power, releases and stops the motor drive dead in it's tracks..I do not get why you would wire in multiple circuits for the control of something so simple.
And the above is true for either single or three phase units. The phase the E-Stop/limit switches is on should be totally irrelevant all control circuit cabling should be on the same phase and the way that is connected at the motor or even the isolator should be totally irrelevant as well.