Could you add a custom keystroke combo for the centre button so it's the same system as the mouse/keyboard hotkey setup. Then instead of calling up the start menu we could have other apps eg deskspace.
That can't happen as, for technical reasons, the Centre Button is generally not the active window (the background is) so it can't receive key or mouse events unless it is specifically-activated. However I am considering allowing users to customise the action taken when the Centre Button is left-clicked. The options likely to be included will be "No action", "Show Start Menu", "Show Desktop" and "Run Task Manager".
Is it possible to add a setting to bypass keyboard/mouse when the pointer is over the taskbar?
No. Simply because if there's one area that users expect a fast response, it is in the toggling of the Dock's visibility. To add such a feature as you request entails adding a bunch of code to detect the mouse's position, to check the taskbar's visibility and taken as a whole this will decrease the responsiveness of the Dock.