There are multiple reasons it looks different.
The map:
He's using a technic called "parallax mapping". Which is creating different layers for the map; the background > terrain > flora > objects (buildings & trees etc.) > the lights > the shadows. Its mostly done with photoshop then maps get imported into RPG maker. The sun rays you see in the game for example, are not actual effects
its just a photoshop layer. This helps him create his own atmosphere.
Assets:
When you buy any RPG maker engine you also get free 2d assets. Most people rather use their custom assets, but as you see here in this forum, people rather use the vanilla assets (like Peasant's Quest) as on top of all the other work for 3d also creating your own 2d assets is quite hard. There are such games with custom 2d assets, I guess all the NLT media games?
They're all RPG maker engine so yeah.
At this point I should also explain that there's a difference inbetween the "pixel" styles and on top of that the pixel art is quite different than the "pixelized" asset.
Chyos is using pixellized assets. And sometimes even just the actual images themselves. Like the tables in tavern are pixelized images but the trees you cut down are just real images.
That mixture gives a unique feel to the game. And it also feels nostalgic for me. Its like 2000s, when developers could not decide if they wanna go with real images or pixels.
Mods & plug-ins:
As
Evangelion-01 said; Chyos is utilizing dozens of plug-ins. If you check the credits, he lists them there, crediting the creators or such plug-ins.
Vanilla RPGM engines dont have such; lets say, crafting system, crafting menu, clock & time gui, quest log system and menu, video player etc. And we know that Chyos is coding plenty of such systems himself. That lets him go out of the boundaries of the engine and increase the quantites and qualities of possibilies for the gameplay.
Even the save system is custom if im not wrong.
Experience:
Well, he's a master with his craft, and thats just that. Can't explain it but only admire as I don't have the same experince.
Btw the 2d models in the game (not lewd scene animations) are just 2d images, cant say they are not models as for the industry lingo, such are considered to be models /mesh. But these are 2d images with a sprite sheet.
Ok thats a little complicated. Lets say for walking animation of your model you would create 8 frames of movement. Starting by the first one you create / paint / model the character and you alter it for each frame to make the movement.
At the last frame you make sure it loops as those 8 frames were a .gif file. And when you import that into the engine and use it for walking animation, the engine itself turns it into a gif. When you walk its just a gif that is animating, when you stop it reverts back to a still image.
With 2d animations you gotta do it for atleast 4 directions up, down, left, right obviously. Some go further and add the diagonal movements too.
With 3d models its kind of... easier... Naahh its not. But atleast the 3d model has bones (hopefully) and if the engine supports it you can just make it walk.
So... Instead of using pixels (like in every other RPGM) Chyos renders actual model imagers for each movement frame.
And hes doing that for each and every character.
I just got tired explaining it
Its a lot of work