It sounds from your question that you aren't asking about the effects of electron flow in the "wrong" direction on battery chemistry, but rather asking if a "positive" voltage can "act like" a negative or a ground. If so, then the answer is yes, it can.
All voltage is relative, so your reasoning is correct. If you connect two positive but non-equal voltage nodes together, current will flow between them.
Calling something "positive" only means that it has a higher voltage potential than something else which you are using as a ground reference.
You can think of it as pressurized cans of air. Let's call 1 atm (which is air pressure at sea level) our reference pressure. If you pressurize one can to a pressure of, let's say, 2 atm, you might say it has a "positive pressure". If you then pressurize another can to 3 atm, it also has a positive pressure. Connecting either can to a 1 atm pressure (i.e. by opening it) will cause air to flow out of it (this is analogous to electrons flowing in the wire) until the pressure equalizes. But if you connect the two cans to each other, air will flow out of the 3 atm can and into the 2 atm can until the pressure equalizes.
So it is with voltages. The electroncs that are under more "pressure" (voltage) will push harder against the ones that are under less pressure (but still "positive", vs. some arbitrary reference).