So the simple workaround actually is to disable snapping, disable mod settings -> map tab -> Snap miniloaders.
The problem arises as a result of the nullius windmills having a hidden entity with a large bounding box which the miniloader then sees and snaps to.
https://postimg.cc/Mv7dGKjs
Another workaround is to place connecting belts (before or after the loaders) since the loaders will preferentially snap to belts over other entities.
A proper fix for most situations might be to have miniloaders snap to the closest entity, or just not snap and keep the placed direction if entities in both directions are found.