It is crazy that you said this game could be around 90 GB. I have Assassins Creed Vahala and it is only 87.2 GB. I am not sure still how your game, which I do like A LOT can be so big when it does not have even half of what Assassins Creed has. This is just an example and I am not talking bad about your game. The size is insane though but I am still looking forward to the rest of your games story.
As one before also had written. The difference is between the games using Ren'py (or any other similar one) and other using a "real" (real in the meaning that they are cpable of rendering a scene) game engine.
Here the dev render a image, save it in an image file (PNG, JPG, WEBP, ...), you load the the image(s) if you view a scene, same with the animations.
In a game with a "real" engine, the dev made the models, world, etc., etc. You have then this saved on the dics, the hotel, Lin, everyone else, the MC, so on and so forth. For a scene the dev only arrange them and
your PC
render the scene. So only the information for the hotel, Lin and everyone else need to be on
your dics. The scene is then rendered with this information and the
description of the scene.
It exist a technique to do that with image too, simple overlay them eg. you have the garden scene with MC, Lin and Jin. You would only need the garden, MC, Lin and Jin as an image. For the scene itself you overlay the garden (background) with the 3 persons (foreground). It can save a lot of disc space, but to do it right is not easy and for every difference (eg. the lighting is different between garden scene 1 and garden scene 2) the dev would need to save the difference or it wouldn't be available and then the scene would lack some quality.