I hope things stay mostly the same, except the amount of food changes based on the difficulty levels. Leave it as is for story mode, and take away most of it for the harder settings.
Same with healing potions. (I usually end up in Grymforge with 80+ healing potions left in my inventory.)
If there's only enough to long rest, say, once or twice before the grove then the player will have to be cautious. And then later, maybe there's nothing much in the underdark except for a few scraps here and there.
That will make the player pay close attention to when the short rests are used up.
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The only issue left is the way the cut scenes are tied to long rests. The more I think about it, though, the less I'm concerned.
1. Most of the scenes don't need to be seen. So what if you miss Astarion looking at the mirror and fishing for compliments? Maybe you'll get it in a later playthrough. That's not a bad thing.
2. Some of the scenes could be combined to happen in the same night. For instance, you can still have a dream sequence after Gale stares reflectively in the fire.
3. Failing the above two points, just tie some of the less important cut scenes to short rests now and then.
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This fixes the problem.
If a player is worried about getting "soft locked," maybe lower the difficulty. Or, since a partial rest is still slightly restorative, it's possible this isn't even an issue.
You know... Difficulty would make all the difference for limiting food. Story is like now, like you said. Normal is enough food for 1 LR and maybe 3-4 SR every 3-6 fights or so. Hard every 6-10 fights. Super hard means you have a hard time finding enough food to long rest even once every 11+ fights. Something like that.
I still think, though, that short rest should be managed by something like HP Recovery/Hit Dice as opposed to 2 hard limits. It would make short rest more meaningful and strategic, allowing you to do SR at the character level instead of the party level, switching out party members when they've used up their SRs.
And I still think camp supplies costing per character causes players to rethink strategically how many they want to keep in party. Why keep Astarion around if he's not doing anything for the party and he costs camp supplies every long rest? Or, better yet, if I know he's going to cost 10 camp supplies anyway, might as well switch him in and someone else out and get some adventuring out of him. I got 2-3 fights out of Gale, so switch in Astarion and give me 2-3 fights from him too, using SR per character to prolong the adventure that day.
SR camp cost isn't as big a deal as the above mentioned items. Make them free still without camp cost. That's fine. But let me use my SR at the character level at least.