Where's it stated that Dorn was still "in charge" when Guilliman introduced the Codex Astartes proposals?
If anything, Guilliman, as "Lord Commander of the Imperium" was in charge of all the Imperium's armed forces, when he introduced the reforms.- the role which corresponds to Dorn's "Warmaster" position during the Heresy.
"Dorn called Guilliman a coward for not fighting at Terra, while Guilliman called Dorn a rebel"
doesn't really make much sense if Guilliman is the one in the "rebel" position.
Concerning Dorn being "canonically the last Primarch"- that doesn't make him the person running the state- the High Lords had already been introduced by this point.
And Deathwatch: First Founding
suggests that Vulkan may have lead his legion for 3000 years:
Some sources state that Vulkan lead his chapter for three entire millennia before he departed on some mission he never declared to the Imperium at large, though scant evidence of any of his deeds throughout that age remain.