The GMAT will never phrase a question that would cause any ambiguity whether the difference between x and y is to be interpreted as x - y or y - x.
Let's look at an actual GMAT question from GMATPrep. I am only including the main stem of a data sufficiency question:
"In a certain year, the difference between Mary's and Jim's annual salaries was twice the difference between Mary's and Kate's. If Mary's annual salary was the highest of the three people, what was the average (arithmetic mean) annual salary of the 3 people that year?"
So here the translation of the first sentence is:
M - J = 2(M - K) , where M, J, and K are the salaries of Mary, Jim, and Kate, respectively.
Even if we interpret this as:
J - M = 2(K - M), we have the same relationship.
In summary, in my opinion and experience, the test writers will not test you on how the phrase "difference between x and y" needs to be interpreted.
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