Both have similar issues....
The 4.6 is just a stroked 4.0 - (they have the same bore size)
Some say the extra bang in the 4.6 cylinder weakens components quicker, but that is speculative. some say the 4.6 burns hotter - but again, the difference is minor compared to the combustion temps already in the chamber!
4.0 GEMS is the base
4.6 GEMS and 4.0 THOR are comparable
4.6 THOR is the engine of choice.
The 4.6 is a fraction more efficient than the 4.0 as you are not on the loud pedal as much.
As long as they have been maintained and the cooling system is up to snuff, they are not bad engines, they are just misunderstood.