Effectively they should argusblybe built separately with the tool designed to make editing easy and flexible and extensible and then have it generate/bake optimal data for the performabt but l ss flexible engine
A concrete example might be the difference between Photoshop and textures in a game. go watch almost any texture artist and they'll have 89 layers in Photoshop but it will all get baked down into just An rgba texture. Photoshop needs to support those layers, layer masks, compositing modes, blend options. The game just needs in rgba8unorm texture.
note:I shouldn't have to say this but because some pedantic person will take issue with this example. I get it's an imperfect example. The point is tools and game engines have different needs. The point is not the specific examole of layers. Another example might be that Photoshop virtualizes storage since it was designed to edit gigiabyte images on machines with 4-8 meg of ram. Game engines, even if a few can stream large images, they are generally not dessigned to edit them