Phaser for a long time was a runtime engine without an editor, and many people missed that type of capability. Same with Cocos2D.
> and that there's no possibility of having a standalone editor.
Tiled (for 2d maps) or Spine (for 2d animations) are 2 examples of well known standalone editors. There's no chance to "make people think" that such things can't exist.
> It seems to be in the interest of "engine" makers to make people think
There's no hidden agenda going on, it's that integrated tools are often much more effective when building things out of multiple different pieces. Wouldn't it be cool to place animated objects in Tiled and see their animation states to properly gauge how they interact with the rest of the scenery in different states? Or use Spine to animate a tilemap going through an earthquake?
Custom file formats exist because features differ, and even for similar features, the semantics differ.