I don't know for sure, but since it's using a built-in Ren'Py feature, and was only added with Episode 11, I would be astonished if it wasn't just counting Season 3 - to count Season 1&2, it would have to either get the data from the 1&2 persistent save (or wherever Ren'Py tracks which lines have been seen) and work out how to interpret it, or create an update to the season 1&2 game files, get you to create a new transfer save there, and then load it in from Season 3 to transfer the coverage figure across that way.
Not completely impossible, but a lot more work than just asking Ren'Py for the coverage of the current game.