The SQL Compare Command Line requires different options to use migration scripts.
You'd need to have created two XML files, one for each of the extended properties we add to the database (storing the scripts location and the migration scripts location), then reference these using the /scriptsfolderxml and /migrationsfolderxml switches. In addition, you'd then use the /sourcecontrol1 and /revision switches.
See the full list of switches here
(and please ignore if it says that the migrationsfolderxml is deprecated, it's still needed I think)