For RSC and Eagles, ECNL's point of view was that the clubs did not have the track record of success to suggest they could support two top/elite teams, so they gave them an ultimatum. I do not think it was geography, more club specific. Since the DA application required all clubs commit to put their top players into DA, it seemed reasonable for the ECNL to protect the level of competition in this way. Some say different, this is my understanding.
It is also my understanding the ECNL has asked clubs going forward to commit that the ECNL teams not be structured as "B" teams -- in other words, a level playing field where kids/families are free to choose the program/team that was right for them (something the DA application did not allow). Having a separate club structure/brand for DA and ECNL might provide that (i.e. Slammers), as would allowing teams and players who want to be ECNL stay (Blues).
It is all evolving, and will continue to do so as US Soccer/DA makes changes to its programs, ECNL drops clubs and adds others, the NCAA changes its rules, etc.