There has always been some DIS-continuity in the old G1 days between toys/comics/cartoons.
The comics likely wanted Hot Rod to be a Targetmaster and then show us stories in the future where he is instead RODIMUS PRIME.
Thats unlikely to be the case with the U.S comic as Rodimus was barely used at all after the TFTM tie-in that was released to coincide with the film. I think he was only used in one other brief story after that, which would suggest that Hasbro wasnt interested in promoting the character.
I dont think Targetmaster Hot Rod appeared much either after the Headmasters story, so it doesnt look like there was much desire to use any version of the character.
He appeared extensively in the UK comics series, but it is well established that Marvel UK were under almost no pressure to use certain characters or to push the latest toys in the pages of their comic.