Scrolling over the connector between left and right side works fine no matter which side has the focus.

So I guess I have to either set focus manually or scroll over the connector....

When using p4merge and diffing the same file the side that is scrolled is getting the focus automatically (which resolves the issue of slow scrolling speed).

So I guess that this could be somehow possible.

EDIT: On mouse scroll I guess you need to identify which side to scroll. So gving this side the focus should be doable. But I don't know how smartgit is working for this kind of use case.