The 3D model will have it's coordinates defined relative to an origin.
If you create a model you should align that origin with the 'origin' of the footprint/package, given in the datasheet, which not necessarily sits at its 'center'.
If the footprint adheres to the same 'creation' rules, both will match perfectly in 3D viewer without any further work.
Most 3D models you get from vendors do NOT adhere to this and are way off origin and usually have the pcb-plane screwed up as well, so need additional rotations to get right.
All new step models @Shack has done should sit correct right out of the box, afaik.