Dan Insanto is a BJJ black belt and in the "Way of the Warrior" documentary series he demonstrated Wing Chun/Boxing/Kickboxing. No doubt FMA play a large part of his JKD, but I think he has a number of influences.
I've never seen or heard of a JKD school that had FMA influence trying to hide it. In fact, most places seem pretty proud that they do FMA??
JKD is hard to define. Some people will tell you JKD has no set form, and "pure" JKD doesn't exist as JKD is whatever you discover for yourself.
"Let your food be your medicine, and your medicine be your food"