Multilayer PCBs also help a lot; it's not mentioned in this article but putting the 100MHz clock on an interior layer with ground planes on the exposed layers would be a good idea.
You do have to design EMC defence in from the start, rather like defensive programming. Sometimes people take the other extreme and cover v1 of the board in extra capacitors, ferrites, TVS diodes etc, then see how many they can remove while still passing EMC. This may explain unpopulated pads you see in consumer equipment.
One of the reasons cheap Chinese Alibaba gear is so cheap is ignoring these requirements. I have a car USB charger that has so much conducted EMI that you can't listen to the radio with it plugged in.