The tooltip is designed to be always visible when launched. It will adjust its postion to be visible when your scrolling makes it out of the window, and unfortunately it covers some of the links.
If you cannot go with this design, we have to customize it to your requirement. I don't think we can easily customize it to let the tooltip to be smart enough to jump to a position that will not hide the links on your page. Although it might be possible that we customize it to stop adjusting its position when there is no enough room for it and allows it to go out of the window and partially hidden, but this customization might be a heavy work.