At least for programming ligatures, wouldn't they tend to be shown as a single glyph (and occupy the same space)? I don't like them, but for people that do, I expected ≠ to be displayed instead of !=, not a different longer glyph.
This is necessary because if all ligatures were one advance wide, you couldn't easily tell the difference between =, ==, and ===, or between != and !==.
Back then, those characters weren't easy to type on dos/windows so it seems to be a case of being stuck with the "lowest common denominator" in terms of character input across OSes, reminiscent of C's trigraphs where "??<" was used because keyboards didn't have "{"—thankfully those are long gone. Ligatures are a hack around that but it always struck me as an inelegant solution.