Mbrooke (Electrical),
We have used the breaker to breaker differential protection for the transformers and the lightning arrestors (LA) in the differential zone. As such steady state of an arrestor is in terms of milli amps. Thus the relay is not sensitive to this leakage current.
When the discharge, it is active for few microseconds only. That means we are talking about the voltage/current burst for the period of microseconds which when converted to frequency it will be in MHz. These CTs are not sensitive to pick up such bursts. Hence such practice is quite safe.