Tools can be smart enough -- it just requires a lot of work and domain expertise. For example, Facebook has used declarative schema management company-wide for over a decade, to manage schema changes for what is likely the largest MySQL fleet in the world.
Then again, maybe this is an area where MySQL's DDL limitations actually makes tooling more possible: there's no transactional DDL in MySQL, so you can't get real clever with ordering anyway. And historically companies don't actually use ALTER TABLE with large MySQL tables; instead they use an external online schema change (OSC) tool which builds a shadow table and then swaps it. Since the OSC tool isn't actually running an ALTER directly on the original table, the exact ALTER is conceptually not necessary, if the OSC tool just takes the desired state as a CREATE instead (as fb-osc does).
That said, I agree with the sentiment in this subthread that it's a complex domain with a lot of idiosyncrasies. I tend to raise an eyebrow when DB tools use generic DSLs and try to handle a lot of different database vendors, as it's extremely rare (almost unheard of...) for a tool's authors to be deeply well-versed in large-scale production experience of many different DBMS. The various communities around Postgres, MySQL, SQL Server, and Oracle tend not to have a lot of overlap at the expert level.