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That behaviour is somewhat expected. The taskbar needs to be always on top normally. I'm thinkig that maybe we need a way to force only taskbars that are not on screen edges to the bottom if a window is maximized to the full screen. Not sure if that's technically feasible, but I will add it to our list and we'll see what we can find out.
In the meantime, do you need the taskbar on that split section? If not, you can disable it by right-clicking it and choosing Multi-Monitor Taskbar > Position > Disabled.
Thanks!