The graphics are not perfectly rendered, so I slightly adjusted .connection_distance, but did not forsee it doing mayor changes to gameplay.
If you open the mod and edit data.lua:
remove the line
base_locomotive.connection_distance = 2
to reset alignment.
This should allow you to use your stations consistently at the cost of slightly more offset graphics.
I may re-render the graphics better in the future, but it is very time-consuming and low priority at the moment.