The problem with making "click in empty space" deselect is that we have "drag in empty space" to modify things. That is good because you don't have to grab little handles to modify things, which is extremely fatiguing if you are doing it all day. Most "other software" as you mentioned

When you drag to modify, the modification happens right away, as soon as your mouse moves 1 pixel. If we were to allow a single click to deselect then we would need to use a "drag square". That is where the drag for modification only starts after moving some ₁₀ pixels. Without this, if you try to single click, the chances are high that you move your mouse 1 pixel or more while the mouse button is pressed and we don't want that to cause a modification.

We've experimented with this and most people really don't like the drag square for modifications because it makes smaller changes more difficult

it isn't clear exactly when the modification starts happening. We could still add a setting for single click to deselect, but it would be disabled by default and would require a drag square.

Note there's spacebar or escape to deselect, or you can bind any other hotkey. Also note that in Spine you don't generally need to deselect, certainly not after every manipulation. Generally you can drag on an unselected object to both change the selection to that object and start modifying it. That is faster than deselecting, selecting the new object, then dragging to manipulate.