I want to say frankly that the entire redesign should be reconsidered. So much of what I see is less usable and attractive to me than the earlier design. Please consider a rollback..
I'd have to agree with this sentiment - I found almost every UX change in 1.9 jarring, and I'm generally pretty relaxed about SourceTree upgrades tweaking the UI. I've rolled back my SourceTree to 1.8 until this gets sorted out.
Specifically on this issue, the extra white space around file rows and the lines bloat the pending file list a lot - on a Retina 1440 display, I get half as many files in view without scrolling as in 1.8.
I fully agree with Kevin. I find it very strange that the Sourcetree team doesn't want to fix this problem. It is a very simple and easy fix, so they must really want to keep the wasteful file list. If you won't even consider fixing this, why not close this jira?