Hello Duncan,
Webench actually calculates the power dissipation in the FET and the juction temperature of the FET at the worst conditions and picks the FET only if it passes those checks. Therefore if Webench has suggested the Siliconix FET, then it would have made sure that the FET would not overheat.
For your design of 3A at 24V boosted from 8V, the current through the FET is going to be considerably large. Therefore the FET's RdsON would matter a lot as it would be directly proportional to the conduction losses in the FET. The Fairchild FET has 17mOhms at 4.5V Vgs and the Siliconix has 1.65mohms at the same Vgs. This is almost 10 times the difference. The Siliconix FET also has a power pad which helps heatsinking very well and consequently helps push the power dissipation limit a little higher.
I hope this information helps. If possibly you should switch to the other FET.
Regards,
Akshay