Integer scale needs to be off in the retroarch video settings. Setting it to on or off in the shader is a personal preference.
Integer scale jumps around a lot and can be quite restrictive on a 1080 display. (It does help with moire.)
The readme.md just explains what the settings do. “Best” is subjective and it doesn’t include any recommendations, for that you’ll have to play around a bit. The defaults are acceptable, until you gain more experience and get fussy.
There is a versioning bug but the end result is the same. (If by, “from here”, you mean the link to the GitHub release.)