I have not used tools.namespace for the reload workflow that it was originally developed for, so I can't say with certainty what the effect on a user would be, but I can make some guesses that you can probably confirm more quickly than I can.
The test case in the patch is one where a few Clojure source files are added to a tracker using function c.t.n.dir/scan-all. No other changes are made to the tracker. At that point, the dependencies are completely correct, and the load order calculated from those dependencies honors them, but the unload order does not.
If that tracker were then used in a call to c.t.n.reload/track-reload, track-reload would call remove-lib on a library B before calling remove-lib on a library A, even though A requires or uses B.
I guess your question confuses me a bit. Do you believe tools.namespace should only create trackers that have load and unload orders that honor the dependencies? Or is that a wrong assumption I was making from reading the implementation?