Hmmm...
Did the fitter look at you on the 61 cm Allez? A 90 mm stem on a 61 cm frame does not sound right for a race fit. You'll want to look at the stack and reach dimension of 58 cm Allez and compare them to the 58 cm CADD9 to make sure you are comparing apples to apples. Using head tube lengths is harder to compare these days for fit with current frame design.
Besides what Ex said, going to the longer stem should make the bike less sensitive to steering input. Especially useful when you are elbow to elbow with someone in a corner.