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I bet ligatures would be unambiguously helpful in programing if they were limited to the presentation layer and controlled by the syntax highlighter.
For example, the author uses Fira Code[0] as an example of well-intentioned by problematic ligatures. The author says this is bad because (1) it contradicts unicode and (2) the substitutions will be inappropriate sometimes.
(2) is solved by applying substitutions in semantically relevant places with the syntax highlighter. This would be particularly useful when typing special sequences. If you get the ligature substitution, then you know you don't have a typo.
(1) is trickier. You want to save a unicode file, and you want to be able to copy text selections that end part way through a ligature. This requires some finesse.
[0] https://github.com/tonsky/FiraCode