I tested this a little. There doesn't appear to be any extra bonus for bordering more than one of a matched number. Matching just one of the the 3 surrounding dice gives the same multiplier as matching all three.
So the points you get for rolling the dice in either setup are:
Setup 4 + 5 + 6 | Setup 6 + 6 + 6 |
1 = 4 | 1 = 4 |
2 = 5 | 2 = 5 |
3 = 6 | 3 = 6 |
4 = 14 | 4 = 7 |
5 = 16 | 5 = 8 |
6 = 18 | 6 = 18 |
This makes your setup where each rolled die is surrounded by 4, 5, and 6 much better than all 6s.