POI's can have a lot of influence on this. For example, at my lowly regional conglomerate, we have quite a difference in autopilot use between certificates. The Shuttle America GOM essentially requires you to use the highest level of automation available at all times, while the Republic FOM says that we should use a variety of automation to maintain proficiency in the various levels. Same airplane, same overall company, but one certificate encourages hand flying, while the other pretty much prohibits it. The difference is in the feds assigned to each certificate. One believes in the airplane, the other believes in the pilots.