I agree with you 100%.
Just to be clear: what we are doing in this Vim conceal (probably many other editors can do the same), is just changing the rendering of the actual code. I consider it a bit like when we write mathematical formulas in Latex, we write code that is not so nice to read but when rendered, it looks beautiful.
And actually, here we could do the same. I remember at SC23 BoF at Denver, Damian Rousson displayed code that had an operator .laplacian. and I was really impressed by that beautiful demonstration of Fortran capabilities. I don’t remember exactly what was written, but I try to write a pseudo code here to demonstrate a bit the capabilities of conceal for what we could do on top of code like that.
On the left is the code that I actually type in my editor (the default rendering that I get with :set conceallevel=0) and on the right I have the same code rendered with the conceal on (:set conceallevel=1)
So you can see that it looks even more mathematical than it was before.
I consider this conceal also a bit like syntax highlighting: we are trying to improve the readability by making the code clearer. So even if I have mapped '%'->digraph, 'call'->phone and '.laplacian.'->Delta, I still type the code and not those unicode symbols (they are only representatives of what is written).
I also agree with what you said earlier: this might be bad for learning the actual tokens… Also I could imagine that this can get out of hand pretty easily and become a huge mess! I would draw the line somewhere in the operators (if one can find good and conventional symbols for them). However, note that when I put my cursor on the line I want to work on, it is displayed as the actual code:

