Just like says. You can still manipulate the area selection box in-game when no area selections remain.

I assume you are in the Simple area selection mode and not Normal? The Area Selection Browser is only used for the Normal mode selections, the Simple mode has its own "global" selection. If you don't want to see the selection box, either switch to the Normal mode (without a selection active in the browser) in the Litematica main menu (middle left), or just turn off the area selection rendering (in Visuals or with a hotkey you can set).