IMHO that's the answer to how to limit long rests, right there. The most important point of limiting rests in Pathfinder: Kingmaker is that time is a factor because of plot events (you get better rewards for finishing earlier, or you get abducted by the evil lich who tired of patiently waiting for you to get to him).
Or the game just ends with "you lose because there's a clock ticking that we've alluded to but you should have known we're going to actually end the game arbitrarily".
I agree time should be a factor, but not like that, please.
I get that Pathfinder KM was very frustrating, because it did not explain this mechanic well, and it did have a game over consequence here and there, but a) that can be easily improved, and b) all other systems mentioned in this thread basically achieve to make resting slightly or much more annoying.
Like in BG:2 you can basically blast your way through each encounter by using all your resources, then put on a podcast while watching your group slowly walk through dungeons and loading screens until you reach open space just outside of Firkrags home, then rest, repeat.
Constantly thinking "man, if I use this cool spell, I have to look at 6 loading screens until I can proceed" is not my idea of fun.
Figuring out how to avoid damage, how to build a group that excels in every situation, how to plan exploration in order to save time, because there are story consequences if you don't, is much more appealing to me. And I note that Larian has already taken a few steps into this direction (buildings on fire will have burnt after your rest, killing those inside. Your infection might trigger, or at least get significantly worse, with each rest, your companions warn you.)
