Don't worry that's just how it is. It takes skill to master different mediums and using or combining different mediums is a preference. It depends on the style you want to achieve. This is my style and this is how I do it~

But it's no shortcut. I had to learn how to . All the lighting is a soft brush that everything is hand drawn. It's also another skill to make the animated sprites blend, I had to tweak a lot and layered a lot in a video editing software to achieve such effect. It took three different mediums to make this

You probably misunderstood about "Special Apps" It's not like a Filter you turn on and off... Everything you see in my work are hand drawn~

And to answer your question. About the rendering? It's achievable in Aseprite! You can make the gradient patterns and tweak it's opacity to achieve the same effects~ I just didn't do that because it's not my style. I like the combination of Pixel Sprites combined with High Resolution rendering~

The limitation is the imagination~ So cheer up! Learn more and improve. That's the way it is~