Ok - I've got SOTN basically playable.
Using the retroarch overlay config GUI (select+X in game) I set:
frameskip to 1
custom viewport width 1440 (x3)
custom viewport height 816 (x3)
integer scale on
hw biliner filtering - turning this to off makes the game look significantly better on my big flatscreen from apx 3 meters away, but doesn't seem to impact performance (disclaimer that I prefer a pixelated look to a blurred look for my scalers)
loading savestates seems unstable until loading a regular game save. not sure if its related to my settings changes or not.