Only the area I am scrolling in to scroll.
Both the area I'm scrolling in and other areas scroll, too.
Chrome 62.0.3202.94
MacOS Sierra

Tested and confirmed that if use Chrome 62.0.3202.94 on Mac OS X 10.13.1 and browse to various sections in Calypso's left navigation menu then switch to a site and try using the magic mouse to scroll just the sidebar that both the sidebar and the primary content area are both scrolled.
Note: if I grab the left navigation scrollbar by clicking with the mouse and then dragging it, the same problem does not happen.
Turns out this appears to be default browser behavior (internal ref: p1512759332000352-slack-calypso). Closing for now, but please re-open if it comes up a lot of times in the future or if you'd like to make a case for a change if that's possible.