Here are some counterarguments:
There can be scenario’s where the agent cannot change his source code without processing observations. e.g. the agent may need to reprogram himself via some external device.
The agent may not be aware that there are multiple copies of him.
It seems that for many plausible agent designs, it would require a significant change in the architecture to change his utility function. E.g. if two human sociopaths would want to change their utility function into a weighted average of the two, they couldn’t do so without significantly changing their brain architecture. A TDT agent could do this, but I think it is not prudent to assume that all actually future existing AGI’s we will deal with will be TDT’s (in fact, most likely most of them won’t be it seems to me).
So I don’t think your comment invalidates the relevance of the point made by the poster.
You don’t necessarily need “explicit self-reference”. The difference in utility functions can also be obtained due to a difference in the location of the agent in the universe. Two identical worms placed in different locations will have different utility functions due to their atoms being not exactly in the same location, despite not having explicit self-reference. Similarly, in a computer simulation, the agents with the same source code will be called by the universe-program in different contexts (if they weren’t, I don’t see how it makes sense to even speak of them as being “different instances of the same source code”. There would just be one instance of the source code.).
So in fact, I think that this is probably a property of almost all possible agents. It seems to me that you need a very complex and specific ontological model in the agent to prevent these effects and have the two agents have the same utility function.