I do have some experience with new ORS…
So Case 1 seems to be a price thing, the total rating is indeed a combination of the average of your LEG A and B holdings, the connection factors, and the overall price. The price for Option 2 is $16 cheaper, and the service in your itinerary legs is marginally better. Comparing a 44 vs a 45 the difference is 1 pt, aka a wash.
Case 2 is quite weird…
One - in Option 2, Leg A: Is that ground network? It makes absolutely no sense to me otherwise.
If it was looking for say Heathrow to Santorini and there is a Gatwick to Santorini nonstop, naturally, Gatwick would be considered. And in the eyes of pax usually, they’d prefer to take the National Express over (or simply go to Gatwick instead) rather than say connect in Milan or Frankfurt. That is the only way I see the 0-rated leg working THAT well. The time difference is because the GN is set to leave at even times throughout the day, and it doesn’t matter as much the time between GN and a flight rather than the time in layover flight to flight.
The other three need to be compared, rather than the second leg.
Option 4 is out, I think, surely? The other two are far superior. I see why you included #4, but the very high cost and bad individual ratings push its competitiveness down.
Then that leaves #1 and #3. And from here some slight speculation.
#1 has a shorter conx time (5h19 vs 1h1), shorter overall journey in air (7h04 - 1h01 = 6h03, vs 12h15-5h19 = 6h56) and more uniform legs (32/32 vs 27/37).
Then we’d need to see the weight of the legs, because for example, if the itinerary was Nice - Fiumicino - Tel Aviv, you’re gonna care more for the rating of the FCO-TLV leg because it’s longer proportionally, and that is a slight boost to #3.
#3 is also about 10% cheaper than #1. And I guess the two-point difference is a balance between those two. Again, I guess.
Image can also fight into this, to some degree, though it would probably be reflected into the individual leg segments.
And an overarching question - is this because your flights do not fill, or is it out of sheer curiosity? Because if there is a two-point difference (for which your competitor might need to fork out some more operating costs, and you still fill your flights (in your particular first case, at an 11% higher price pt), then you’d end out the true winner there, regardless of the ORS result, surely?