It's not related to Tooll.io, You are on Win 8/10. If you want Taskbar behind, you have to use 3rd party tool: 7+ Taskbar Tweaker. It's for advanced users only. Read manual before use! Anyway it works PERFECT on W8/10 (with any fullscreen software).
I feel your pain. The behaviour of the window-frame component of the different Windows version is a pain in the butt. Interestingly enough, I can't reproduce the problem with my Win10 system: