I think you may be overthinking this. I'm not an expert on the comics, but I'm thinking that there is no Malcolm/Barry twin character in this story. My guess is it's like this:
Eobard Thawne/RF is Eddie's descendant, hence the reason he didn't kill him. Wells is Eobard/RF, and he can be in two places at once because he's clearly a time traveler. The RF we see beat the crap out of Wells is either a past or future version of him. None of the characters on the show realize this though, so that's why it will likely take them a long time to realize RF and Wells are the same.
The only feeling I can't shake is that all of this, even the scene at the end, is a red herring. Wells seemed too obvious from the beginning, and even though it seems clear now that he's the bad guy, I feel like there is something else we don't know.