For me, the placement of certain options is more of a problem than the graphical layout of them.
For example, I always instinctively go to "Playback" to look at how my files will play (on double click play all/ play selected etc.), and then realise that they arent there. They are actually in the "General" section. The "Behaviour" and "Advanced" parts of the "General" section should be in "Playback".
"Tree & View" should be renamed to be a bit more encompassing. Maybe just call it "View". And inside it can have everything it has now, plus maybe the options related to images (Raw image settings). The "Track Images Location" (now in File location) could be put there too (and renamed to "Cover art location").
The "Ouput file location" could be moved to "Library and Folders", and the "Tempory file location" moved to "Encoding", and then you could ditch "File location" altogether.
In terms of graphics, if you are going to use twirly arrows, then I'd have them twirl to show whether they're expanded or not.
Or perhaps you could go with some kind of pane interface, so that rather than expanding twirlys and having to go down through a list of options, you start at the left and have the most general groupings ("General", "Playback", "Startup" etc.), then in the next pane just the headers (that currently have twirly expanders on them) which you select to see the detailed options in a third pane. That would be a very clean interface, and being horizontal based, might negate the need for any kind of scrolling at all.