Getting Subsites to point to Domains and Subdirectories

In trying to accommodate a collection of legacy sites, I want to be able to map certain subsites of my multisite to point to a domain, while others will point to that domain with a subdirectory. The multisite is setup with subdirectories, so for example, subsiteA would have an alias of domain.site and subsiteB would have an alias of domain.site/subdirectory. We were successful in altering the MU plugin, but it stopped working with 4.7.3. Appreciate the guidance on this.