Should the super be on top or underneath and presumably no excluder.
Where do the bees put their stores naturally? For millions of years without doubt? Above the brood nest of course!
That is where I leave their stores. Can't do it any other way, as it is all on the same frames for mine (14 ×12). Does it affect their survival? No, not at all. No risk of them not crossing the gap between the frames for mine, as the stores are all on the brood frames! On occasions an extra super of stores has been left on, but not often.
No excluder during the winter. A risk of them leaving the queen on the cold side.
Some put a shallow box of stores under but if I were to want the shallow back, it would be a super again, simply by inserting the Q/E and leaving it like that for three weeks in the spring; in my view unnecessary and lazy (just for the beek's convenience) by the beekeeper and unnatural for the bees. And no problem for me of getting bees to move into a super in the spring, either.
Leaving honey means there is no chance of sugar syrup getting into your honey next year. I recall my first year while I was not aware of the sugar syrup problem and shared the crop from two of my colonies with my mentor - he had an awful lot of sugar syrup! I only realised that the following year!
My bees collect plenty of ivy nectar usually. Haven't actually fed sugar in the autumn for several years and have had 25kg of fondant in boxes for about 4 years now, so only fed about 8-10kg during the winter to colonies that needed it for some good reason over that period. I usually have a few spare frames of stores which can be swapped into colonies which are short of stores in the autumn or placed in a box below the brood box in time for them to move it up ready for their winter slumber.
I leave my bees in peace throughout the winter - no disturbance means no broken propolis seals or agitated bees. They consume relatively small amounts of honey stores while clustered in well insulated hives, most stores being consumed during the spring expansion before any good flow.
Isolation starvation, in my limited experience, seems to occur when they have started brooding and there is a very cold snap in early spring and they do not forsake the brood to follow the food. Usually smaller colonies suffer more than the stronger ones but not always.