it is my understanding that the 2 digit number is required by some US states for licensing purposes where a passing score is a 75. The three digit is used by most residency programs/other states. The passing there is 182-184 or somewhere around there.
People will often mistaken the two digit score for a percentile. In reality a little math shows that it could not be possible for that to be true. (e.g. with a mean of 216 and sd of 24 for step 1, the top 1.0 % would be very roughly 2.5 sd above the mean or 278; in reality, starting around a 240-245 people get a 2 digit 99, so this couldn't represent the 99th percentile; these numbers aren't exact but they serve their purpose in getting my point across). Also on the NBME website they reiterate this point.