Is that same problem, i.e. you want to be able to diff your diagrams or do you want the actual data format embedded in your document.

If it's the second, you can embed XML within SVG or a PNG. If you draw something simple in draw.io [0] (which I do co-author) and then "File->Export As" either "SVG with XML" or "PNG with XML" the diagram data is stored within the display format itself. This way you can just reload the SVG+XML or PNG+XML and carry on editing. But the PNG and SVG display as you'd normally expect.

Does that solve your problem?

[0] https://www.draw.io/?splash=0

Yeah, I feel this pain too. MJD's Linogram might work. I've also tried writing the diagrams as Python to produce SVG, or in D3 (to produce SVG), which both work reasonably well but seem like a lot of work.

It should be easy to do flowcharts in pic(1). It's also more diff-friendly.

GNU pic can target LaTeX directly, if that helps.

I use draw.io, and export to xml.