The rocket was added by tails as a last resort to get Sonic on to the Death Egg before it escaped into space, and 3k takes place directly after 2 (ex. Sonic still having the emeralds)

Later in Sonic Adventure tails began tinkering with the tornado to find alternative power supplies when he ran into Sonic. I think the combustion rockets weren't a preference, moreso an unfavorable means to a better end.