My suggestion is create an "iron ration" that you need for a long rest and limit when you reward them, for story beats that would be like 4-6 encounters. Each long rest needs an Iron Ration and since they are limited, Long Rests become valuable. Need to bump of short rests to like 3 between a long rest.
Of course, if you are going to limit long rests, you will need to rebalance the encounters so they are not all hard / deadly.
What if the player gets stuck and cannot rest, being on the verge of death / before an extremely difficult fight? Read my previous post why this won't work.
It would be easy to reset counters allowing rest before "boss fights" (possibly on lower difficulty settings though)
Well, not every tough fight is a boss. It's hard to say what will be a difficult fight for some people. I had no problems with the minotaurs myself, but the fight with the goblin leader was extremely unpleasant. There is a reason why PoE2 doesn't have rest restriction items, unlike PoE1