Yes, making a tileset is directly related to JCS because of the limitations of the JCS editor have importing graphic. If I weren’t working in JCS when drawing tilesets, I wouldn't have to limit myself to less than 256 colors and such a narrow canvas that is the pixel size of a tileset.

For example, when I make importable graphics for Warcraft 3, I create icons in templates or recolor model skins/textures using alpha layer with no color limitations at all. The defining argument is that there are specific settings for when you make graphic for a level editor, which defines which level editor you are using.

It’s only because the JCS editor is limited in what you can do with it that you see creating tilesets as something that’s “not a part of the program” because drawing tilesets is literally the only other part of the editor. Other programs, like the one I mentioned before, have much broader options for customization, creating terrain in a third dimension would be the equivalent to JCS’s 2D level creating, but also has the ability to modify game events using JASS, modeling, texture imports and customization of game constants (e.g. how much damage a specific weapon would do in Jazz2).

If we had the source code, we could open up tons of new doors in the JCS as well. But that is going too far off-topic. =p