Yup, this Rodimus was intended to be a different character than the G1 Dark Hot Rod, who had been created by Megatron.
This is more of a physical manifestation of Rodimus's insecurities, given a body by the clone synthesizer.
Rodimus's difficulties grappling with the responsibilities of leadership have been a pretty prominent focus
of the character in additional Japanese fiction, such as Macrocosmic Seekers:http://www.e-hobbymagazine.com/category/english/exstoryen
This is also a great read, if you haven't seen it yet.