Already did that. Though, I can't say for certain how up to date the patches are on the version I have. There's no releases on github, not even an alpha. Had to just randomly hunt down a copy off google from who knows how long ago. Don't even know how people got ahold of that either.
I don't know if the dev(s) are trying to keep it hidden or something until it's more stable, who knows. Guess might just have to wait for a public release whenever they feel it's ready.
The configs folder is in the repository here, you can just clone the repository and get the folder, or just manually download it from there itself. Also make sure that none of your folders or roms have special characters on their names, since GBArunner3 doesn't support loading those characters in filenames yet. I've just tested the games you listed on both DS and DSi and all work completely fine.
As for "keeping it hidden", is just that is not stable enough yet for even an initial release, and the main dev (Gericom) is focused in another project right now. GBArunner3 for in its current state is meant for testing and developing, that's why you have to compile it by yourself in the meantime.