ExGM don't worry about the port match, unless you can see air molecules
altering an intake is tricky business. Creating any angle greater than 7 degrees really monkeys up laminar airflow, if the step is facing toward the port I doubt very seriously that it will effect airflow and might even help if there is a some intake reversion. I say seat the lower manifold and see if there is any overlap by the gasket or intake port which would inhibit flow, if itgs clean bolt it down and bolt down the upper intake.