Right now, it's not possible to save those settings separately.
However, even if a setting is not present in the .CFG file, it doesn't mean the sim won't use it, it only means it will use its own internal value. And, settings that are not relevant to P3D, won't be used anyway even if they are added to the .CFG file so, as long as you set all the other tweaks to values you want, this shouldn't be an issue.