Being tight, I wouldn't have given them back absolutely all the honey! But it is perfectly fair to give them some of the fruits of their labour.
Putting it under will probably result in it being quite quickly moved up into the brood chamber. If (when) they empty all the honey out, you can remove the shallow box. The 14x12 should have plenty capacity for the winter.
BUT, you need to get that brood box well-filled with syrup (and some honey) ASAP.
Your BB having zero stores, the full super will provide only about half their winter needs, so you need to get at least 5kg of sugar (made into heavy syrup) in there, before the weather gets too cold. You might even give them Ambrosia. As I said, I'd have pinched some of the honey - but I'd have repaid that debt, and more, with Ambrosia.
Oh, and don't go cutting down any Ivy for another month or so!
And since you have a slightly under-strength colony, DO fit a reduced entrance (if its not there already) and it would be good to give them insulation in the roof - as early as you can.
Its not wholly true that the smaller colony will need less stores for the winter. They will certainly need more per bee ...