I believe population of country, general DEVELOPMENT status, along with of course the soccer-specific culture (quality of soccer development) that you mentioned were major factors if I remember his assertions correctly.
I do remember that he says that when you throw England into this formula their predicted playing quality (domestic players) is about what you see now. Not that they are underachieving as some people think.
So your Nigeria example would suffer at the general development and probably soccer-specific development factors.
Now, Stephen Szymanski is a Chicago-based Brtitish American economist. He famously hates the MLS model and stupidly accused it of maybe being a ponzi scheme. Which he has since walked back. Just thought I'd throw that in there.