After executing bin/cake migrations upgrade the following info is displayed:
Upgrade complete!
Next steps:
1. Set 'Migrations' => ['legacyTables' => false] in your config
2. Test your application
3. Optionally drop the empty phinxlog tables (re-run `bin/cake migrations upgrade --drop-tables`)
this is a bit misleading as bin/cake migrations upgrade --drop-table won't work with that config option set due to this if statement.
I'd remove the first step here completely and only show it after the old tables are dropped.