I'm almost certain that the game does track individual soldiers' experience. Hence why the experience sometimes goes down. Similarly, I believe this is why units tend to do better experience-wise in Autocalc; it picks the men killed in the unit at random, while in battle the most experienced are at the front and most likely to get killed. That last bit's just speculation on my part though.

I'm wondering, if the experience is known for each soldier individually, does that mean that the combat/morale bonuses apply differently to each man based on his experience, or does the entire unit fight better because of a few highly experienced individuals?