747Classic
Yes, many airlines do have Performance Engineers on staff, or use a sub-contractor. This is particularly so in Australia where local regulations are close to, but not entirely equal to FAR25 / JAR-Ops requirements. In other cases, the AFM data is so 'user unfriendly', that the local authority has stipulated presentation of data for operating crews derived from the AFM.
Up to a point, I agree with Mutt that "Technology has taken us beyond that requirement", Boeing for example is now producing much more 'crew friendly' data. The cr@p still delivered from some other manufacturers still meets all of the certification requirements in full, but would require much much crew manipulation to be daily useable. (I would like to sincerely thank these cr@p providers, they've kept me in a good second income).
The instance you cite of Company derived differing speeds for the same aircraft PROBABLY arise from the (non-Boeing) performance engineer adapting Boeing supplied AFM data to either accurate and/or conservative interpretation as I've alluded to earlier. Both are probably correct (one is more correct) with the more conservative simplified case leading to performance penalties that the operator finds acceptable.