I think there's likely little difference in the EMI generated.
The main difference is the the Zener has to absorb all the inductive energy in the top circuit, and transistor absorbs the energy in the bottom circuit.
Actually, the main purpose of he Zener clamp is to protect the transistor from overvoltage, not to reduce EMI.
I don't see how.
Leakage doesn't contribute to RF noise.
All that diode does is increase the voltage where the zener starts conducting by about 0.7V.
Such an added diode is needed if the Zener is connected directly across the inductor.
(For the connection the Zener and diode would be inverted, with the diode cathode to the plus voltage, and the zener cathode to the bottom of the inductor.)