Well there ya go, I stand corrected on the Armada cartoon front. I will admit to having all the DVD's but haven't really watched them enough to remember all the details like the above.
I guess if you take it for granted that Primus and Unicron are the same species as each other (transforming metal planet gods) then the Mini-Cons are the same as other Transformers, just not natives of Cybertron and a different species. They were just introduced to Cybertron by Unicron in the same way rabbits were introduced to Australia by early colonists - not native but certainly not a completely alien lifeform.
Oh and that has always bugged me a bit - the fact that BW characters were suppposed to be Micromaster sized, and were indeed portrayed as such like when BW Megatron flew over a deactivated Soundwave, but in comics like IDW were portrayed as equivalent size and some of them disguised themselves as big creatures such as a T-Rex yet with no discernable size change between modes.