The short version:1. They choose to dig too readily - digging through 30 layers of solid earth and rock is preferable to the AI than going through just two scrap and wood walls to reach an open shaft.
2. They dig too quickly. It took me ages to dig that deep with pick and shovel. They did it in in seconds with their bare hands.
3. Wandering hordes can see you through a lot of earth & rock. I would be happy if this privilege was exclusive to the Blood Moon horde.
The meandering long version:
This was a random horde that turned up while I was building those personal quarters, not a horde I saw coming and I could have prepared for by going into my defenses and picking them off. They turned up while I was doing the "build your personal quarters under that bunker so that it covers them." part of your plan. When I first heard them, I went up to the bunker because I thought they were on the surface - by then, they were already underground. I couldn't see anything so I assumed the horde had wandered off. I went back down. I heard them again, and realised they were digging down to me.
The bunker is 5 X 5. I was in a 1 X 1 shaft in the dead-centre of it, about 30 blocks deep. The bunker covered it completely.
If my bunker/tower was something like 10 X 10 instead of 5 X 5, maybe they would have attacked the walls instead of digging under them. But I don't think I could build something that big (and still be as solid) by day 19/20.
The only real difference from your defensive bunker over personal quarters plan is that my "defensive bunker" is on the surface. Personally, I prefer to fight them on the surface: more options for escape & less digging. But it seems equivalent to me. If my whole base had been underground, I think they would have done the same thing - they'd run up to the first solid defenses through those clear pathways you mentioned (traps do not stop them, in case you haven't see it yet

), and then I suspect they would evade the defenses by digging further down and beneath them to get to me as I was constructing my 'personal quarters'.
NB - I'm very happy with A17 by the way, I'm just adjusting. I think I'll have a 'defensive base' and a 'crafting/storage' base that aren't too close to each other. In previous alphas, those two areas would be one base. If a horde turns up at my crafting base, I will try to move them to my defensive base, maybe by shooting them from an elevated walkway or something. Or just jumping down and kiting them
Or a sky-scraper with concentric rings of defences. I tried that a few months ago in A16 when I first heard about the digging. It worked quite well, but these new super zombies would have smashed that base