Take a look at the Configuration hierarchy. You can have the overlays per-system if you add them to the system's retroarch.cfg file. For individual games, you can use the game override in RetroArch to set the overlays.
@caver01 Your link actually dropped me off at the most recent post and I scrolled back from there. While the last picture I see is definitely more scanline than the first screenshots, the second to last still shows a lot of pixel separation.
I guess I'd have to see ut in action on my own television before I can tell if it's really more enjoyable than the current setup of crt + smoothing (yes @BobHarris, I do that too now), which is why I figured I'd just try it if it ever got into a RetroPie update.