Ever since then, scrolling in Transmission covers up the button I use most-frequently—the Show in Finder button. I can't tell you how many minutes have added up from all the times I've had to move the mouse away and wait two seconds for that button to become clickable again. It is very annoying.
I don't know what the best fix is, but moving the buttons up above the progress bar, having the progress bar extend all the way to the window edge, and leaving just enough room for the scroll bars to appear between the window edge and UI buttons seems reasonable.