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The most likely function for the synth component in regular Gen 3 synths is to support teleportation, since that's the only known function of the courser chip which looks exactly the same (and we get a courser chip installed in our Pipboy to let use access the Molecular Relay and teleport while sided with the Institute). For non-coursers, it probably just doesn't have all the same permissions for requesting teleportation.
X6-88 doesn't appear to drop either one upon death, but if he had anything it would be a courser chip rather than a synth component, since he's a courser.
In the case of the ones that turn up as random infiltrators in your settlements, they're exactly identical to a regular settler in almost every way except for counting as allied to an attacking synth force (which usually gets them slaughtered by the other settlers) and now having a synth component upon death. Mechanically, being a synth is just the game tagging them as a synth, and you can even get ghoul synths.