Ah, yes, that silly "P42-9" nomenclature. Sorry, but no such thing. That nomenclature is merely an invention by the railfans -- I have never heard anyone from either GE or Amtrak ever refer to the locomotive as a "P42-9". The official nomenclature used by GE is P42DC. This is what is seen on all of GE's documentation including maintenance manuals, operators manual and parts catalogs.
A Dash 9 is a Dash 9 and a Genesis is a Genesis. A Genesis is NOT a Dash 9. Yes, they have many things in common, however if you look at the evolution of the Genesis series, the P42DC is basically an upgraded P40 (btw there are several different nomenclatures for the P40's, I don't think GE or Amtrak could ever agree on just one). The P40 has its roots in the Dash 8 series, specifically the "500 series" P32's. The divergence point in which the Genesis series came into being was well before the Dash 9 came on the scene.
The major differences between a Dash 9 and P42DC, besides the obvious carbody, trucks, number of axles, etc; the traction motor gear ratio, engine cooling system, HEP alternator and control system, locomotive control system (specifically the software). The Genesis series (P40, P42DC, P32ACDM) incorporated a number of "firsts" for either a passenger locomotive or locomotive in general. For example, IFC computer screens (P40, one of the first applications), electronic air brake (Amtrak #809, one of the first applications), 7FDL12 EFI engine (P32ACDM, the first, and only production application). The two California owned P32's were retrofitted with EFI for their 12 cylinder engines, but this is the only retrofit that I know of for a 12 cylinder FDL.
To answer the original question, yes the same diesel engine is used when comparing P40's to Dash 8's or P42DC's to Dash 9's (Dash 8's mechanical governor, Dash 9 EFI). The only difference is in the engine control for the passenger application whereas the speed schedule changes for supplying HEP. When providing HEP, engine stays at a constant 900 RPM's.