There isn't much difference between running out the fill hole and just touching it.
Fill it until the level is just at the bottom of the fill hole. The fill hole is horizontal so you can't really over fill it without a lot of extra effort.
On the rear diff, if you jack up the back of your 4Runner, don't put the drain plug back in until you let it off the jack, and be prepared for more oil to come out while lowering your vehicle.
I drained the differentials while the vehicle was level. The I pumped the exact amount called for in the manual. Each bottle of gear oil had a clear side window and ounce scale, so I could see how much I was pumping in. None of them got overfilled.
