I would set your mains to small and you can keep them at 40 if you like or move them up to 60hz like many of us here have them at. If you like the small setting better than the large or vice versa then run them that way. If Audyssey found some reason to set the surrounds to 100 I would wonder why as Audyssey set mine to 80. I would be inclined to say you could easily drop the surrounds to 80 and see if it sounds better or worse then go with the one that sounds the best.

Jason
M80 v2
VP160 v3
QS8 v2
PB13 Ultra
Denon 3808
Samsung 85" Q70