I haven't studied this, but my gut feeling is that there's a difference in kind between a "field of study" and a "theory". Aether was a theory, which was (AFAIK) discarded when Einstein came up with special relativity as a better alternative. But alchemy was much bigger than just one theory or even one philosophy, and it's not all "discarded as false" by any means.
What we mostly associate with alchemy today is the hilariously elaborate idea of the "great work" that culminates in the creation and use of the philosopher's stone. But that whole theory was a relatively late (Renaissance) invention, born (I'm guessing here) of some alchemists' ambition to be taken more seriously as scholars by making it seem as if they had a grand, unified plan. Long before that, people were doing "alchemy" for smaller, practical problems such as manufacturing and construction, and they did perfectly good work that's still visible in modern practices. For instance, the alchemical terms "sublimation" and "calcination" are still in use today, with their meanings basically intact.