the old MArvel Comics had a much better take on the " post season 2" stuff.
Hotrod, Magnus and the rest are targetmasters, and simply out there in space.. I don't recall Rodimus prime ever existing in the Comic continuity.
Optimus does die... more than once.... But Hotrod never Becomes Rodimus prime.
HOWEVER, in the comics, There is an alternate timeline where he does become Rodimus prime... and looses the war to the decepticons, then being led by Galvatron ( who is a reincarnated Maegatron, created by unicron, much like the movie). who after conquering Cybertron, returns to earth, and stripmines all of its natural resources, kills 90% of the population, and more or less just stomps heads in for the fun of it.
He Kills Rodimus prime.. and grows bored.
Eventualy, in the "normal" timeline, Unicron uses his godlike abilites to comb the timelines seeking for one where he is victorious.. and finds that one. He then reaches across space and time, and grabs Galvatron from that timeline, pulling him into his timeline. And asks him to repeat his actions there, and conquer cybertyron, wiping out the transformers, and Primus for him again.
You see, in the main timeline, Ratchet Sacrifices himself to COMPLETELY DESTROY megatron by getting them both stranded inside a space bridge ( or so everyone thinks, for a while... They do both... EVENTUALLY come back...)
, so there is no megatron for unicron to remake.
HOWEVER, Galvatron instead decides to Take on unicron, and destroy him, so he will never again be under someone else's heel.
After megatron comes back, we end up with both Galvatron and Megatron existing at the same time, as two more or less different characters, with Galvatron being the "older and wiser" of the two.