If you read the USMLE website, it states that they have changed the 2-digit scale to appropriately reflect 3-digit scale. Therefore, not everyone who scores 230+ is getting 99 and 2-digit is more comparable.
With that being said, the website also states that starting July 1, 2011 the 2-digit score will be only reported to the test-taker and the state medical board where the applicant might apply. No other third-parties such as residency/fellowship programs will see your 2-digit scores.
In short, 2-digit score will only be reported to you and the state medical boards. I don't believe that residency programs were using 2-digit scores to compare applicants in the first place because of the 3-digit score variations that might be present among 2 99s.