They are generally automatic in v5.
The manual tool might be left in to be able to connect a crossing that was originally meant to be not connected or was drawn such that kicad assumed it is not meant to be connected. (A point where two wires cross without connection converted into a junction where 4 wires meet.)
Another reason might be to protect against possible bugs of this new feature. Or simply because it was there in the past and removing it felt wrong. (Choose your poison.)
In this case it was done to generate the screenshot. As mentioned above: There is normally no longer a need to manually add junction dots unless you made a mistake while drawing the schematic. (Might speed up a fix as you only need to add a junction instead of removing the offending wire and redrawing it such that it connects.)
I am more and more convinced that case 2 should not be handled by ERC but by the junction tool itself. (would also prevent stuff like @Sprig showed from happening.)