The higher Z will give you better lows since the transformer inductance is higher but it could reduce high end response due to extra inductance and leakage inductance. Also the power to the final will reflect different loads on the mudulators.
You will get better positive peak capability using the 12K taps. With the 18K taps, the modulator will probably just barely be capable of modulating 100% if even quite that much. The transformer will have more step-down using the high-Z primary than with the lower one.
Since the secondary winding will be working into the same load impedance, I wouldn't think there would be a great difference in frequency response between the two sets of taps.
OTOH, the modulators will operate at higher efficiency using the 18K taps. At the same power level, the modulator tubes will run cooler. But for voice modulation that shouldn't be a problem.
I believe this is an off-the-shelf unit, not custom built for the KW-1.
I would recommend the 12K taps.