I think the greatest benefit in using the ball is that it encourages you to move more. I like having a chair with back and arm rests but then it’s too easy to just stay in one position for long stretches. Ideally I would like to be able to switch between both in the office but then space becomes an issue.
I did some research into the chair vs. exercise ball debate: http://www.somastruct.com/exercise-ball-versus-office-chair-comparison/ and I saw at least one study that said the same thing you mentioned about the ball becoming uncomfortable on the backside. It might have something to do with the increased surface area of the ball. It’s not something I’ve experienced. It might be worth inflating or deflating the ball slightly to see if that changes anything.