I just realized that SaGa games are a possible example of an alternate progression system: They don't really have levels. You have HP that increases now and then seemingly at random, you have base stats but they don't really change except through equipment, and you get more powerful by gaining new skills/empowering your current ones.
I just did a sidequest dungeon here in Sea of Stars (the rematch against Romaya to free the duke) and it provided extra EXP, which got me an extra level. I was doing some other sidequests and picking up some "ultimate" equipment too. Thinking about it more, it just feels like the progression system (in this case, levels and exp) is pretty tightly managed here. The stats from leveling up are a subtle enough difference that you don't really feel much more powerful after each given level-up. You also don't really have any experiences of fighting a more-powerful enemy that you can come back later at a higher level and find them noticeably easier. You do get a bit of trouncing weak enemies, IF you backtrack through certain areas (which is also rare unless you're doing it for fun or hunting for treasure or whatnot). Story and area progression are gated just as tightly as level progression (and as said above, they're tied together, in that an area will level you up to its base pretty quickly and then get you back on track).
In Sea of Stars's case, I wonder if it's not just a case of the game being as linear and guided as it is, including the way it organizes battles (non-randomly, non-respawning). I think that has a big part of it too, since the game knows exactly how many fights you can/will get into and your exp tracks directly to that, so even what level you are and when is just part of the baked-in design instead of a reflection of your choices. I think that's the crux of it, really. But again to be clear, I didn't tend to avoid any fights, so I suppose if you did so you could do a challenge run at a lower level (but not every fight is avoidable, so I don't know to what degree that would change things).