Unless you are comparing two different sets of items to then have a couple of differences and the differences are the same, I do not get it.
This would be analogous to: 12-9=3, 7-4=3. Here we have the same difference.
The problem is, I really don't think the average human is comparing two differences when using the term in question.
Best Answer
Same difference is an idiomatic oxymoron [Oxford Dictionary Online]. It effectively means
SUPPLEMENT
The Urban Dictionary defines it as follows:
The Cambridge Idioms Dictionary defines it as