Hell, even The Witcher 3 did this incredibly well. Spoiler incoming for those who haven't played it yet.
"The Bloody Baron" quest not only has three endings, IIRC, but one of your choices can lead to entire village dying. And I'm pretty sure there's a few other variables that can end up having some effect at later points in the story.
Granted, it's probably the most-cited example of great Witcher 3 quests, second perhaps only to the romancing options (again, 3 possible outcomes), but I've already come across a few more main and sub-quests where reloading and trying a different option was meaningful.
As part of the journey, they might not affect the ending, but in an RPG style game with quests, it's just as much about the journey.
In this game the lack of choices mattering is apparent from the beginning. Most gamers may not care but for a certain type of gamer, this is a game ruiner.
For example with ME3 again, I had fun the entire way through the game, assuming my prior games' choices mattered. And there actually were different dialogue options, references to past choices, etc.
The ending was awful, and I will never replay that game ever. But if my choices didn't matter even while playing, before the ending... well that's just an awful game to a person like me. I would never play a minute of a story-based, choice-based game where I know the choices don't matter.
What's the point of the map, if all you're concerned about is which ending you get? If there are 40 choices with an average of 3 options each, it's still obvious before you buy or even hear anything about the game that it won't have 12,157,665,459,056,928,801 endings.
You can definitely have N number of choices contribute to 2 or more endings and still have every choice matter.
You can have 100 choices with 3 options, and have all of the make an impact on the ending and still only have 2-3 endings. Or any number of endings between 2 and n (in your case the 12*10^m.
Have each choice do a +1, 0, or -1 to some internal metrics.
You could call this a good or evil system, but it could be a ton of different things. They could be doing +1,0,-1 to corpo, streetkid, and nomad rankings.
Some choices might do +1 to streetkid and nomad, and 0 to corpo, you could have any number of combinations. Or you could have 1 choice do +10 to corpo.
Then at the end, whichever had the highest score would be your ending. Or you could do if highest was 10-30 points, you'd get 1 ending, but if your highest was 40+ youd get super ending. Like if you were mostly corpo, but still a bit others, maybe you become middle management in final cinematic at corpo X, but if you were like ALL IN on corpo choices, maybe you'd become new president of some corpo Y.
That way every choice matters, and you can still have a few different endings. And the 'vanilla basic ending' being where you are choices were mostly neutral, or what they guessed majority of playerbase would choose.
But what OP was saying, is that 98% of questions have 0 impact on anything. Which makes them not impactful and not matter at all, and that often is boring.
edit To rephrase, I don't even think it's about the endings at all. Most of the choices in the game do not actual change the trajectory of your character. Most of the decisions put you on the same track. Kill steve, don't kill steve, even if it seems like it mattered to some part of the story, it actually did not.