Most of us still loft or moat our bases.
While we can do better than ever at defenses, mostly, because you have to repair and don't want to lose animals etc, its largely still a game of prevention.

There are new things since you played fro the sound of it. the iron cage is a wood-wall-thin but made of iron piece that takes a lot to destroy, and its see through, good for your livestock and there is a gate for it. Needs a roof or it will rust, though.

There are also new defenses, one of which shoots anything that moves (including YOU).

2) the problem is really livestock. Nothing that flies does much damage, unless you count mistlands. I am not sure about THAT raid, I got a flier with it, but it was in the zone and probably a stray not part of the raid. I am pretty sure that a cube of iron cage with iron gate and an anti-rust roof plopped on top is all you need to keep livestock safe from any raid, assuming you go out and fight.

3) I am not sure about the mistlands raid. I got 2 pseudo-fliers, but they are melee critters that honestly can just 'jump' really well. I don't know if they were part of it, as I was IN the ML when I got it.