Large Targets, Flying, Charging

Lets break this question down;

1. Models who are Large Targets (like giants and dragons) can see over other non-Large Target models.

2. Flying models can charge over other models and scenery to engage models who are further away (it says so in the rulebook).

3. Models on hills can see over models on lower ground. This is how archers or war machines on hills can be screened by infantry on the lower ground, and still be able to shoot.

So, putting all that together means the following things, flying models can charge units on hills even if there's enemy at the bottom of the hill screening the ones at the top. Or as you said, if the flyers are at the top of the hill, then since they can see an enemy unit that's behind another unit, the flyers can indeed charge that enemy.

Large Targets can see over other troops and can therefore be shot at even if you have a (normal sized) unit screening the large target unit. Thus, large targets could charge enemies who are behind screens or other units, if it were not for the fact that units aren't allowed to charge through any other units (even through skirmishers. Although Kroxigor can charge through Skinks, but that's something else entirely!).

However, a large target that is also a flying unit can charge enemies who are behind other units because it simply flies over the unit in middle, in the same way that normal sized flyers can charge units on the top of hills.

And yes, charge reactions would be exactly the same.

Hope that cleared everything up!