Unfortunately, Dynamo is not clear about this at all right now. Those numbers are actually in square meters. Everything in Dynamo is in SI units unless otherwise specified. And by “otherwise specified,” I mean that the unit would be displayed along side, like “12 sq ft”.
The units display setting in Dynamo affects numbers that have units associated, and this mostly happens when quantities come from Revit directly. However, the Surface.Area node is from the geometry library, and it doesn’t know anything about Revit. It returns only a number, not a number with a unit, so the number is as if it were in SI units. You could see a difference more directly by comparing numbers that have units with those that don’t.
It’s on the development track next year to clear up this confusion. We have some ideas, but how would you like Dynamo to treat numbers vs. numbers with units?