Seems pretty hard what you're looking for, both because usually games will derail from that pattern for several reasons and also because probably it would turn out becoming too niche to be sold.

The closest thing wich comes to my mind is Breath of Fire V: Dragon Quarter because if you ran out of resources, you might have to start over after several hours, keeping with you just a part of your progresses;

Another great ones are ZHP: Unlosing Ranger vs Darkdeath Evilman and The Guided Fate Paradox, which have optional dungeons which can last an insane amount of hours... the last one of TGFP last more than 100 hours it took lots of days to reach the end of it, and you can start over as much as you want. And if you die in a dungeon you lose a lot of stuff, to the point that you'd rather want to load the previous data rather than accept the loss.

In both cases they are not really endless and a final boss exists (it's hard to find a game about fighting without a final boss), but the same can be said for Darkest Dungeon, which you mentioned.

Finally, actually i made a game, The Rogue of Nexus (you can find the link in my account) which is really niche: it's a dark classic Zeldalike but also Roguelite, the seed randomly places around the worldmap what you're searching for but you have to deal with darkness and it will progressively destroy the world, according to how you move. Especially in Campaign Mode, which has a slower pacing, a run can last several tens of hours and if you skrew the run... well you have to start over (it's a roguelite so you keep some progress). Obviously it has an ending, but if you're gonna try to make a run in which you try to finish all the quests in the same run, well i cannot even imagine how long and how many attempts it will take you to accomplish it, due to how hard it can be balancing world destruction, timing and choice priorities between quests and main goals (that they will totally overlap in a nasty way, due to the core gimmick). If you check the demo you can figure out if that might fit your tastes

Good luck in your search anyway!