all voltages were spot on and the phone appears to charge at its typical rate
So there is probably nothing wrong with your assembly.
Was the MintyBoost tin out in the open while charging, or sitting in a backpack or some other enclosed space?
I would also be curious about the charge current from the Minty to the phone. Some phones will try to pull more current than the Minty can deliver. But the boost chip usually shuts down before the batteries get dangerously hot.