There are really two problems you need to solve here: does the story have enough differences to make a second, completely separate playthrough worth it, and is the gameplay loop solid enough to enjoy the playthrough a second time (or more depending on the number of differences).
If it's just a scene difference, it's a lot easier to save scum it than start over completely to see it. Now, if those choices effect later scene visibility, based on a scoring system most likely, you force the replay to see everything. This could annoy players, as the game needs enough changes to be worth it besides just missing scenes. If it's something like Ren'py, they'll just skip to choices and make different ones (if they care enough at all), or if there's a scene replay they'll just ask for a completed save with all options open so they can watch it there. Making the story have enough significant changes between one playthrough and another is akin to making multiple games using the same/similar assets, so it could take a lot more time and effort along with the impatience of players wanting their specific routes finished before you worry about the other ones. There are some games making it work, but they're few and far between.
If you find a way to make the story worth going through multiple times, the gameplay loop has to not deter people from playing it again as well. VNs are probably the easiest for this since all you need is for the story to be different enough and just as compelling as the first run through their choices, so long as you avoid any kind of grind if it's a sandbox. For things like rpgm, you do have the benefit of players hopefully enjoying the battle mechanics (again, as long as you aren't forced to grind too much), but if it's just a walking simulator it'll probably lose people immediately on a second playthrough.
Tl;dr it's a lot more difficult to create a game that's worth playing through multiple times, and save scumming is honestly easier considering how most options don't affect later content.
