Can the Dock bar reserve it's horizontal space even if window is maximized?
If you try to make a window bigger than the size left by the Dock, by dragging the bottom of a window yourself, you will notice that you can't do it. This is because the Dock already behaves like a Windows Taskbar: you can move windows behind it but not resize windows beyond it.

The problem lies with the tool that you are using to resize the window-it is extending the window more than it should do. Try using a different tool to do the resizing or resize the windows yourself.