Wait, I think I found it.
My version has ENGINE=INNODB at the end of each CREATE TABLE statement, but the Liquibase version doesn’t. When I add ENGINE=INNODB to the Liquibase version, it does create the foreign keys.
I’m not sure what ENGINE=INNODB does or why Liquibase doesn’t add it. Is there a way to make Liquibase add ENGINE=INNODB to all the CREATE TABLE lines for MySQL?