Reading them it seems to me like a lot of "clones" would fit neither in the first list for being too close to the games they're cloning but also not in the second one for being too different. Things like Widelands or Unknown Horizons come to mind.
I'm not familiar with Widelands or Unknown Horizons.
The only thing is whether a game makes an effort to be faithful to the original. So for example, SuperTux doesn't qualify as a clone of Super Mario Bros because it's in many cases doing its own thing (e.g. auto-run, switches) with no regard to that. That makes it an original Mario-inspired game rather than a clone.
Similarly, SuperTuxKart draws a lot of inspiration from the Mario Kart series, but doesn't attempt to emulate it. (STK, by the way, I'm planning on adding to the distinguished games list once I've had a chance to playtest the new version... which I didn't even realize was already released. Whoops!)
But just as an example, OpenTTD would be on there if it wasn't already on the distinguished games list, since it's a faithful reproduction. And something like Penguin Command or XScavenger is still on there despite making minor gameplay enhancements and tweaks because it still remains faithful to the original overall.
BORED games
I see you haven't been exposed to modern board/card games. None of them have libre video game implementations, but there's a bunch of them you're missing out on. Just a few examples off the top of my head: Battlestar Galactica, Dark Moon, Secret Hitler, Werewolf, Ticket To Ride, Fun Employed, Qwixx, Plague Inc, Love Letter, Hivemind,...
I go to a meetup every month where we play board games like these, and it's really fun. I think it's unfortunate that so many people's idea of a board game is something simplistic or badly designed like Monopoly or Candy Land.