We always use a pair of (bipolar) transils to protect the transceiver from overvoltage. However, this is a protection, overvoltage still causes malfunction (but not damage).
Of course, it does. The tolerance in the transzorbs (I guess that is what you refer to) wlll cause the common mode to generate a differential.

Even with isolated transceivers there is a need to establish a common reference (gnd).
That is plain common sense.

Erik