The brown color seems like an odd choice when put next to the sleek silver gradient of the column header bar, this isn’t enough to say that it is a bad design, or ugly — but it is a bold choice that I don’t care for.

Agreed. However, I would argue having any bar – no matter the color – above the keyboard would appear “heavy.” That is not to say the toolbar should not be there; it needs to be there. You can consider said brown bar, the “power bar.” Also, as Ben mentions in his article, ‘File Management’ could use some work; the iWork suite got it wrong (and in this case, so did the Omni Group).