ToxicTiger, recursion is now disabled at the start of the game. You can unlock recursion by researching the Recursion 1 and Recursion 2 technologies. If you don't want recursion, then you don't need to research those technologies.
Wow that is actually a interesting idea. Maybe MagmaMcFry should implement that in the next version. Maybe if you place down another factory building in another one then it would create a ladder on the side or something. Of course I know nothing about Factorio modding or lua in general, and don't know if it is possible.
It should be very possible since its already in the mod. Just have to redesign the stacking factory research to add a stairs up or down thing and graphic for both and walla.