So Felltower has some factions, but it also has a little bit in the way of conflict arcs.
Good vs. Evil
There is a very, very strong Good versus Evil conflict in Felltower. It's central to the game design. The PCs generally are on the side of good, although not always. But there is capital-G Good in direct and indirect conflict with capital-E Evil. Some of that evil is consciously fighting against civilization and good, and some of it just is in a way that is orthagonal to Good . . . Elder Things often fall along that line.
Although we joke constantly that Magery is an evil trait, there isn't a "religion" versus "magic" conflict in the game.
Caution vs. Confidence
The game demands confidence, and risk-taking. The game punishes hubris, and thus caution allows one to live long enough to take risks. Overconfidence is an easy -5 points but it could cost you your character; Cowardice is an easy -10 and it could cost you any real success.
This does show in NPCs, too. Goblins - and some of the monsters and factions - show a bit too much caution. Conversely, NPCs such as Sterick as a good example of when confidence becomes hubris, and he ended up paying for that. Maybe not in the way a reader or player might think.
Old vs. New
This one is less obvious, but there is a conflict between the new and the old in Felltower. Many, many things in there are old. Some are ancient. Many of them conflict with newer things. There is a confict between the needs of the veterans and the newbie PCs, too, even if they're on the same side. They have different needs, driven by the XP system. Those in the dungeon are often in conflict between the needs of those who have been there a long time, and those who have more recently arrived.
This is also expressed in aging and passing of the guard. Some things are holding on for dear life; others are in ascendence. Again, this is less obvious, but it's quite real.
We don't have any conflict between civilization and barbarism - fantasy style, anyway. We don't really have Law vs. Chaos, except embedded in Good vs. Evil. We also lack any conflict between nations. If I can think of any conflicts I'm missing, I'll add them in a future post.