Not a definitive answer, but a guess:
The free agent logic you describe is for Major League FAs. And you say you don't have evidence that confirms one way or another.
So what if the system treats IFAs the way it does Minor League FAs? ie; it evaluates the teams' Depth Charts and sends the player to the weakest one where he has the "best opportunity" to succeed.
I hope not, or everyone in your world is going to start manipulating their player positions.