It's easy to tell which FATEs are linked by the fact that they only last 10 minutes unlike the rest which are 15 minutes. I notice this myself and deduced that you need to clear one FATE to make the other pop. That was apparently SE's solution to make token FATEs pop, but nobody noticed until Yo-Kai. Now that this has been discovered, people doing beast quest can rest easy now since these FATEs are triggerable, so to speak. I never did the FATEs in Western La Noscea or Southern Thanalan, but just look for the 10 minute FATEs and do them to pop the token FATE.