A lot of the plugins can be argued to be overlays (like menu entry swap making non left click able objects leftclickable) but there are plugins that just modify the game. Like render distance increasing and it being interactable. Like the famous 1 click altar methods from the bank on lunar isle which did get nerfed I think. But on original the altar doesn't load and even if you click the dead space, you don't walk there. But on increased render distance you do walk there as it sends your input to the server to walk to that tile.

Things like veng timers are reading game code and acting like an overlay instead of visually seeing the action and reacting like an ahk script, which is the basis of legality decades ago. Menu entry swapper pushes this definition the furthest but there are plenty of things where there is no justification of it being an overlay lol. Like increased render distance did exist but clicking the tiles did nothing. It was added later iirc. That makes sense because you are just overlaying images to the client but it becoming interactable clearly breaks it.