You are for sure going to want the Em with the second and third fingers because you'll need it for barre chords. Also super easy to grab the C that way, which is a frequent combo, Em and C. I'm not sure what the benefit is to the other way -- I recall wondering the same when I took Lisa's course. Obviously both is ideal, but if it were me, I'd say prioritize the second and third finger version.
"I got this guitar and I learned how to make it talk."