If you want the site where the MainWP Dashboard is installed to be accessible over a certain port (e.g. https://my-mainwp-dashboard.com:123456), then that has to be configured on the WordPress side, since that part is not MainWP-specific.
After that, the development team can take a closer look and see if some tweaks can be applied so that the MainWP Dashboard is not accessible when using ports other than that one.