Yabai wiki (which serves partially as the project's documentation) it does explicitly call out the usage of the mouse to change the window layout:
If you resize a tiled window, yabai will attempt to adjust splits to fit automatically.
When you drag a tiled window onto another, yabai will either swap their positions in the window tree, or modify the window tree by splitting the region occupied by the window. The action is determined by drop-zones; 25% of the region towards a particular edge will result in a warp operation towards that direction, and the center (50%) of the window will trigger either a swap or stack operation (based on the value of
yabai -m config mouse_drop_action). See this picture for a visual illustration.
Additionally, yabai can enable you to move and resize windows by clicking anywhere on them while holding a modifier key.
# set mouse interaction modifier key (default: fn)
yabai -m config mouse_modifier fn
# set modifier + left-click drag to move window (default: move)
yabai -m config mouse_action1 move
# set modifier + right-click drag to resize window (default: resize)
yabai -m config mouse_action2 resize
With focus follows mouse, you can also focus windows without having to click on them. This can be set to either autofocus (window gets focused, but not raised) or autoraise (window gets raised as if it was clicked on). Focus follows mouse is disabled while holding the mouse modifier key so that you can access the menu bar easily.
# set focus follows mouse mode (default: off, options: off, autoraise, autofocus)
yabai -m config focus_follows_mouse autoraise
Mouse follows focus makes it so that when yabai focuses another window (e.g. through a focus command), the mouse cursor gets moved to the center of the focused window.
# set mouse follows focus mode (default: off)
yabai -m config mouse_follows_focus on