Call me OCD, or something less polite, but I like to have all of my tracks the same size; consequently, this drives me nuts:
Suggestions:
a) Just extend the scroll bar to the end. Add an option for the Master track to be scrolled or not, if you think it's potentially confusing.
b) Just lift the Master track up to match and leave some non-scroll-bar-colored blank space there.
Cheers.