I don't know how it actually played out in his mod, and I'm not sure on his implementation, but I assume he added many new minor civs that cover the independents of a particular area. Provided they have together the same amount of units as the previous independents, it's not much more of a resource drain and shouldn't impact gameplay at all. Actually I already plan to do something similar for flavour if certain minors are well known enough (Moors, Poles, Tamils ...).