Is it acceptable to use "just as well" in an academic paper
I don't see why you couldn't use that phrase. To make it less colloquial-sounding, simply take out the superfluous "just":
The exchange might as well have taken place in Abu Dhabi.
And then it is in a plenty good enough register for an academic paper.
Since you mention it, it does sound a little informal to me, and the phrase "might as well" would be a little distracting to me since it sounds like the idiom, like "might as well get used to it".
You could try "could as well" instead, but then it wasn't too bad to begin with, either.