Because in the cases ligatures are used most prominently, a "logical" character is made from multiple characters.

Nobody expects mathematicians to write all their formulae in ASCII either, they are allowed to use special markup to denote specific things. Why can't developers use more specific notation for displaying code? We use `==` for equality checks due to a limitation of typewriters, not because it's the only sensible way to do this. Give ligatures a chance for a single afternoon, and you'll see the value of purpose-specific glyphs. They aren't replaced by arbitrary hieroglyphs, but actually self-explanatory, helpful representations of the thing a bunch of characters are supposed to tell you.

But the programming language is token-oriented.

But keyboards are not. Even if I’d be able to convince the maintainers of my favorite programming language to also accept some Unicode glyph as synonym to ‘==‘ how do I type it? Ligatures might not be ‘the right’ solution, but they are a highly efficient approximation. Also the cost of reversing the decision to use them is basically zero.

That's what I said. To the programming language it's just a token and representing that with a single ligature is fine.

I replied to a comment, that the document is character-based and therefore ligatures are inherently wrong.