That part of the book (Contact) really bugged me.

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.

I haven't read the book, but...

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.