The way to consistently use 'm' as thousand and 'mm' as million is if you assume a Latin derivation, with 'm' short for mille. https://en.wiktionary.org/wiki/mille#Latin ('mm' thus being 'thousand thousand', since roman numerals don't compose that way -- MM would be two thousand).

That doesn't mean that that's the way it evolved, but it's a way to categorize it mentally so it makes sense. While there's no logic for it conflating with 'million' and 'mega', at least 'mm' is fairly unique, unless you measure your money by its length.