Does anyone know why some of the older models 2008 and earlier are set up different-some have short drivelines between the transmissions and transom assemblies and some look like standard hookups directly from transmission to transom assembly. Is it a CG issue that they learned later on?

Yes better CG, I went threw it when I upgraded to bigger power. I put in 12" drive lines,not cheap to do.

CG is very important... The full rigging and configuration is taken into account as the boat is built. Some need longer drivelines than others...and yes, some boats with "light" engines were built with plug ins...