While I understand some of the design decisions that were made, I agree with others that this is a poor decision or at least not a complete solution.
For years, I have been using Parallels and have chosen to keep my windows taskbar parked at the top of the screen and hidden until needed. This has worked great for me. Now with Parallels 9, I have to keep the windows taskbar visible, but it is only half visible. I can't hide it, because then it becomes completely invisible and a pain to bring visible. This is a horrible design.
It seems that you have made a design decision based on a use case for one version of windows (both 8 and 8.1) which impacts every version of windows used and every user, regardless of how they normally use the task bar. The "solution" provided earlier is by no means a workaround and is very weak.
I would venture to guess that the majority of your users are using an older version of windows, including Windows XP, Vista, Windows 7, and multiple versions of Windows Server. To penalize all of us for a small group of users that might be using Windows 8.x makes no sense. You have made Parallels an inferior solution as a result.
I would highly recommend at least adding an option to allow this new "feature" to be available only if chosen by the user. At least only those people that have Windows 8.x will be affected.