Any thoughts, ideas or comments to help me choose?
I’ve walked both, but in springtime. They are similar in some ways — lots of off-road walking (though the Madrid may have more), great albergue structure, no pilgrims.
For fall, I would choose the southern route.
So much of the Madrid takes you through wide open agricultural fields, which will all be brown and harvested. But the towns are nice and the hospitality much appreciated.
The Mozárabe, whatever the time of year, has Nely and the Amigos extraordinaire. There is no other route that I can think of where the amigos group is so heavily involved in the infrastructure (they have built most of the albergues themselves) and so committed to taking care of you if you want to be taken care of! Also, since the scenery is more mountainous in parts, and will have fewer brown fields (but many many olive groves), I would find it more enjoyable to walk in fall.
I don’t want to get into the realm of unsolicited advice, but just to make sure you have considered the Invierno from Ponferrada and the Geira from Braga to Santiago, because I think both of those are excellent choices for fall.
Buen camino, Laurie