This article is very interesting in lots of ways. For me it raises a whole lot more questions (when MLS would get involved, how it seems that some teams benefit a lot more than than others and how that is fair etc) than it provides answers as to how involved MLS is when certain players are signed. This came up most famously with Dempsey when the league might have paid the entire transfer fee, or part of it or something else. Who knows. Same thing happened with Toronto and Urutti. This new wiz kid GM at Toronto who was previously in the MLS front office.
I really hope more digging can be done on this question (and the whole MLS rules maze in general which this is one part of)