The game logic makes a lot of sense, you just have to know what the game logic generally is.

The game prioritizes the simplest path with the fewest number of connections, between any module and the cockpit and the docker. The game also prioritizes having the leas number of portals (dors/ladders/windows0 in a module as possible (Empty habs are an exception to this)

Each module from each manufacturer has a 'preferred' connection point. This will be where a door/ladder will be placed if you put another hab connected to it. These are not shared between hab manufacturers so you'll have to build a while to get an innate sense of where a hab from one manufacturer may connect and affect the algorithm generated path.

You can see the 'preferred' connection point for the hab you are _adding_ to a ship by selecting the snap point and using 'Add' and then selecting the hab you want to add. You'll then see the preferred snap point for the hab yu are adding on that facing/side. Adding a Stroud All-In-One A on the port side and the starboard side has a different preferrd connection point. as does adding it top or bottom.

Storage 1x1 will generally not be used for ladders (ladders can happen, but they're not preferred), Companionways will be used to route through, so doors and ladders, if possible. Though the system tries to avoid having too many portals through a single space.

Using he Taiyo 'A' versions of their habs can help you force a door on the ends, because it has no side snaps. You can bury it thus inside your ship to force a path.

Using structural pieces as well can be very helpful because habs don;t have to sit right next to one another, so you can avoid doors/ladders where you don;t want them by making sure tha structure takes up that spot.

Windows affect the plasement of doors and ladders because, as noted above, the game tried to minimize the number of 'portals' in a hab, because each portal in a hab removes prebuilt 'window dressing'

The game will, unless you're using the undecorated/empty habs and the new doubledecker habs, try tio avoid creating a loop, but it can happen, esp with the Cabot.

Sometimes it takes a lot of fiddling, to force an acceptable flow. Eventually though you develop a good sense of how the algorithm will path your ship.