I can't find any rulings about the models getting in the way of each other. The YT is much larger than its base and I find that the model is often in the way (touching) other models even if the base is not. What is the ruling for this? Do you just remove the model from the base and follow the rules as applied to the base itself? Or is this considered overlapping.

Only the base has any effect on game play. Models touching models do not matter. Only bases overlap. So yes, if the YT model is in the way of other ship models, simply pop it off the base to clear things a bit.

Jim

This is a very common situation for me and I just follow the advice on the rulebook to modify the number of pegs to increase or reduce the Falcon’s height

It's in the rulebook that if two models touch, just remove a stem section from one of them so that they can pass over/under one another.