Well, with just silver it honestly wouldn't look terrible if the engine bay was grey and the rest of the vehicle was a different color. Most of the dual color 4Runners were another color and silver, so the cladding and fenders were silver and then the other color for the rest. I don't think it would look weird to have a silver engine bay and another color for everything else if you really liked it.
I do agree about the door jams though. I saw a 4runner that was a green like imperial jade but when I opened the door to get inside the door jams were a different color and stuck out so bad it kinda ruined the effect. Engine bay wouldn't do that though for me.
At the end of the day, we are just dudes on a internet board, it's your 4Runner!