I would imagine that it doesn't do it with manual transmission because when you're stopped, the car either isn't in gear, or the clutch is pressed in, so there's no "pressure" (for lack of a better word) on the drive axles. With automatics always being in gear, there's always forces acting on the axle, even when stopped. Unless it's in park or neutral, which is why the vibration goes away. I think it's some kind of resonance vibration that only happens at that low rpm. I can't explain why it goes away when I creep up a bit and stop though.
I'm worried about the vibration wearing something else out, is why I'm concerned.
I know what you're sayin about the Subarus, or at least the GT's. They do seem to have their nuances, maintenance wise, ie. what fluids you use, or having to replace all 4 tires if one goes down. Seems like there's always something more to learn about them. But, I personally don't mind. It's still my favorite car I've ever had.