Why seprate Flarum and Laravel tables ? You could just connect to the same database with Laravel.
Then choose where to put migrations. You could put all your custom migrations in your Laravel project and just make sure to run them after Flarum (also, you'd need to alter the migration runner so it can use two different migration tables as they aren't compatible between Flarum and Laravel yet share the same name), or use a Flarum extension just to provide migrations and have all of them managed by Flarum with a single migrations table.
As it has already been said many times, there's no easy way to use Flarum as a Laravel package. But connecting to the same database should work fine.