Ah, that's a good point! Maybe it could also set a very low opacity so you can still see the faint outlines of the boxes (would need to test how this looks, maybe it'd actually better to just hide them all).
Btw, quick solution in the meantime to achieve the same functionality: just open your browser's developer tools console and type in the following:
$$(".prodigy-content g").forEach(el => el.style.opacity = 0)
And then set it back to 1 to show all boxes again:
$$(".prodigy-content g").forEach(el => el.style.opacity = 1)
(Because you're only modifying the opacity of the current boxes, you can even keep drawing new boxes while the others stay hidden.)