The definition of pi is what determines the digits of pi, FULL STOP. There's no room whatsoever, for any sort of agent to 'leave a message' in those digits. I would think even a full-on theist would be embarrassed to suggest otherwise.
All the agent needs to do is design or adjust the life forms it wants to find the message so that they are inclined to choose a numeric base in which the right sequence appears in the digits of π. The definition of π defines it's value, but the sequence of digits doesn't just depend on the value, but also the choice of base.
The control implied is basically the power to create all the universes laws (and the math we can learn in it) from scratch.
Back then it hadn't been decided yet if the distribution of the digits of pi are such that all finite numbers can be found in it or not. Some years ago I read about some proof that they can. That means that "Carl Sagan was right!" in whatever encoding you like can be found in pi is you look deep enough.
The thing is what does "deep enough" mean? If we consider some two digit decimal number, like 27, then the chance that it isn't the first two digits is 99%. The chance that it isn't the first two nor the second and third digits is 98.01% and so on. The chance of not finding it among the first 500 digits is less than 0.6%. But unlikely things can still happen, so finding a message "too near the start" might convince some people that pi was created by an intelligence but wouldn't really be a good proof.
The point was that this is what proof of a Creator would look like (and the aliens suggested there were others).
It was, IMHO, a giant gauntlet thrown down to religious folk. And elegantly done, too.
I would be curious to hear more. As far as I know that is still a conjecture.
Aren't the digits of pi randomly distributed? So then, you can encode literally any message you want by picking an offset into them. Could even design a "compression" algorithm where a message is designated by its offset, though I'm guessing it won't be very efficient in practice.