The installer hasn't caused any issue to the scenery.cfg. Your reference to a "traditional installed area", seems to indicate you are installing into P3D 3.4 or 4.0, which means we are not using the scenery.cfg anymore!
However, if you installed coming from an old version, the installer has "migrated" your old installation into one using the new method of the add-on.xml.
At that time, it had to *remove* the scenery area from the scenery.cfg, because now the scenery will be referenced from its add-on.xml file. If, at that time, your scenery.cfg was already corrupted, usually because you edited it by hand, or another product or utility corrupted it, the installer haven't touched it, so the old line is still there.
You can just reply Yes to the suggestion to remove the orphaned area and the error will go away.