Everytime I look away from my villagers they find their way into whatever hole, crevice, pit or other unreachable location they can find

there is no way down or up from there and I'm sick of having to baby proof everything

Don't let them walk through water as they are not fast swimmers and often get stuck in water unless you push them out, I'm no expert on coding nor on pathing, but water should be a last resort to get anywhere, like the absolute last choice an npc decides on going. and the wandering characters (like guards and unemployed) should avoid it all-together. I've also had problems where characters would just sit outside of the wall where their bed is on the second floor, and then go, "I can't get home I need a new one" which is frustrating to say the least. I'm not sure how to solve this, or why some npcs get the message and others do not but definitley worth looking into pathing anyways.

Past that Npcs should not be allowed to take 2 block (or greater) falls willingly, the lady that got stuck on the top of the church as a prime example, I now have to build a fence up at the top of the bell tower or some way for people to get down and that's obnoxious, and there have been plenty of other instances of similar situations enough for me to bother to make a github account and complain

Yeah, it's pretty bad. I don't think they have changed the pathing that much. It's basically the same pathing method that vanilla MC villagers use. To me, by far the worst part, is that half the time, they can't find their beds at night. Specially if you have multistory buildings. I once built a huge mansion for me and my family, and had to build a staircase for almost every room, because they would just stay in the lower floor facing a wall, sometimes looking up at the ceiling above where their room is, and incessantly say they can't find their way home. I love the mod, but villager AI is just not suitable for a mod like this. It either needs it's own independent system, or a strong rework. And as for the water, a simple workaround would be to make it so the npcs can only go into the water if the player is commanding them to follow him, for example. They definitely shouldn't go into water. Not to mention that toddlers and other small npcs tend to drown sometimes by getting stuck under a block that's underwater.