One thing to keep in mind is that it's better to shim a one piece base. That way the whole base is at an angle and the rings are still in alignment with eachother. When you have 2 piece bases and shim just the rear, now it is elevated above the front shim and your rings will not be aligned properly. I always lap in my rings but that only accounts for a few thousandths, putting in your shim will throw you off whatever thickness you put under there and it's too much to lap in. Now when you tighten your rings around the scope you are putting uneven tension on the scope body which can lead to trouble. I feel the one piece is the best way to go for shimming.
Having said that, I have indeed shimmed the rear base of a 2 piece system myself and it seemed to work ok. In theory though, it's not a good idea. At least that's my opinion.