I don't doubt that existing graphical languages have very poor tooling.

I believe that diff tools could be better if they operate on some format that represents the meaning of the code, not the details of how it's written. New tools would have to be written, so it's largely a matter of pragmatism and momentum that prevents such a thing.

FYI I googled "WebMethods Flow merge tools" and one of the more useful discussions actually featured you from 3 years ago expressing similar sentiment: https://news.ycombinator.com/item?id=12106945