I'm sorry you're having issues with the lot. The issue might be because you're not working with a level lot, maybe? The house looks good. Are they able to get into it now?
I don't know that I've ever built directly on that particular lot before. I usually build in a temporary save on a smaller lot and then place the lot in my play-save, some times on a bigger lot.
Now with saying that I do remember doing just that, building a house and adding it to that lot in a few different saves.
This how-to linked here - How To:
Build a Basement Under a Foundation. It shows how I build a basement, but also shows how I build houses. I basically lay down free flooring as an outline so to speak. Making sure to add free flooring where I want stairs to go for front/back porch/deck. This way when I go to place the stairs they don't dig into the ground or whatever.
I could try help troubleshooting? But feel we probably have different building experiences because of the different ways we build.
Lapaige, I see how-to links in your post. *Wink* I found a couple of how-tos of yours about stairs and CFE and added them to your post.

— Edited to Add:
I did some troubleshooting and am not able to recreate the same building issue. Thinking more due to our building styles. I took some photos to share anyway. I'll delete these later if you'd like?


Made a simple box house with the flooring a little bigger than the house and stairs. Left the flooring for the photos to show how I make room for the stairs.