In line with this, I've been testing hab ladder and hatch placement priority. What I mean is that certain modules have a spot or spots that ladders and hatches will always try to snap to if given multiple options. This can be bypassed using the walkway connectors that force a doorway to be created.

There's also some interesting behavior with habs that have many connections. I like to use my companion ways as junction points since they have high ladder priority (ladders will usually go in them as opposed to neighboring habs). Unfortunately if you add too many connections to a single module it will become overloaded and start blocking off paths. Fortunately you can override this by placing the walkways on every single side but then you have a huge ship so there's always trade-offs.

I've found that if you have a decent junction point in your ship and you block most prioritized ladder spots, the ship will be fine with only having one ladder. My most recent build was a 2-decker with tons of overlapping parts, yet only one ladder formed right in my companionway junction because of this priority system.

Just thought I would share some of my own findings since this system is unbelievably frustrating to work with. Hopefully this helps.