In the dynmap there are many layers now, with extra layers that classify them. What I suggest is that these layers toggle all the layers in their category, for easier enabling/disabling of layers.
I assume you mean the [[[Main Layers]]] heading, if checked/unchecked, enables/disables the players/worldborder layers?
Unfortunately, it’ll most likely not be done. It requires an extensive research and time to make that happen. We’ll be better off re-writing the code for the Dynmap website.