No real reason, but it would stand out as clearly artificial
It shows a little more sophistication than counting, and could serve as a useful touch stone for future communication...
The idea has history...
for instance- If you suspect that the species is visually oriented from the format of the message it sent the use of primes could be a clue for them to decipher pictographs that you transmit...
In reality you would use a format as much like the one you received as possible...
you could send back a copy of the message you received - that would be a clear signal that you received and are thinking it over...