You state this like a fact. A GUI might be your personal preference but markup is preferred by many. It takes me an order of magnitude longer to learn where all the buttons are than it does to internalize markdown syntax from a few good examples. In a GUI you spend time futzing around with visual details, In a markup chart you spend time building and communicating a coherent mental model. The difference in output quality is apparent to me.
There's an analogy to programming: sure we have visual programming tools but who uses them? they break down when things get mildly complex. A markup driven charting tool lets me edit in the comfort of my chosen IDE, check it into source control to collaborate, renders live instead of checking in an image artifact, and has clearly-defined semantics (ie not just a pile of incoherent boxes and arrows). IMO, it's superior in every way except fine-grained control of the layout (which is a fine tradeoff for me - I want my readers to focus on content - consistency is more valuable than styling). If your purpose is communicating complex ideas (not making a pretty picture) markup-based charts have some distinct advantages that you just can't get from a point-and-click interface.