Transformer coils in series, switching for 12/24V. EMF killing my circuit?
Switching an inductor may make it work like a boost converter, and thus temporarily generate a higher voltage.

One way of making sure that the input voltage to the LM338 converter is no higher than allowed, is to wire a high-wattage (between 600W and 5 kW) TVS diode with an appropriate clamping max voltage biased against the input voltage and ground.

Also, if you're switching on the measured/actual output voltage, then you can get into oscillation. It would be safer to switch on "desired" output voltage, and let the regulator make sure it gets there. You could perhaps feed the bias voltage from the regulator ADJ into your microcontroller with a resistive divider to achieve this. Or you could just use a comparator with a pre-set trip point to drive/un-drive the relay.