That raises some questions.
First, why is there a difference? For any given sequence of numbers both of those layouts requires the same amount of movement, just mirrored around the 456 line. There should be no physical reason for one to work better than the other, so it would seem it is something mental. What is that?
My guess is that it has something to do with our left to right then top to bottom reading order. If someone speaks out loud the digits from 1 through 9 in order and you are asked to write them down in a 3 x 3 matrix as they say them you will probably fill them in reading order, giving 123/456/789.
Second, it would be interesting to see what would happen if the order within the rows were reversed, 321/654/987 vs. 987/654/321. My guess is that the latter would beat the former. It gives a less complicated sequence when accessed in reading order.
Third, I wonder which layout would have won for calculators if the calculator makers had tested like Bell Labs did. Let's assume it is a given that we have to go with either 123/456/789 or 789/456/123, and just need to determine which works best in a calculator.
With the phone all you need to operate it are the digits (the first touch tone phones did not have the '#' and '*' keys).
With the calculator you also need the decimal point, the operator keys, and '=' [1]. The layout of the digit keys needs to fit well with the layout of the non-digit keys.
I'd guess that '=' is the most used key, with '+' the second most used. Third is probably '-', although I'd not be shocked if it was 'x' because it will see a lot of use in percentage calculations which might be common enough to put it ahead of '-'.
Because '=' and '+' are so important, it makes sense to put them somewhere that can be identified by feel, and the best place for that is probably one of the bottom corners.
If that's where we put '=' and '+', then I expect calculator order in the 3x3 digit grid would win, because of Benford's law [2]. Calculator order would put the smaller digits closer to '=' and '+' than telephone order would.
[1] or 'ENTER' if you are civilized.