I wouldn't say "most" use ATF at all. Back in the day, the Chrysler A-833 4-speed (still one of the sweetest-shifting manual transmissions ever, especially when equipped with a Hurst rather than Inland shifter) came with the recommendation to use ATF UNLESS "objectionable gear rattle" was audible in direct gear under acceleration, in which case a typical 75w90 gear oil was recommended. I think the GM/Muncie "rock crusher" transmission had the same recommendations. Don't remember about the Ford top-loader.
Most modern manual trannies seem to recommend either 75w80 or 75w90 GL-3 gear oils.