When you scale to -1 to mirror, and then Freeze Transformations, the normals flip.

They do for me anyway.

Try Display > Polygon Component Display > Normals to view normal direction.

I do not personally like the Mirror Geometry command. I find more controlable results to simply move the pivot point to the mirror junction and duplicate, scale -1. Then I usually, Freeze transformations, Reverse Normals, and Delete History (in that order).

Good luck.