Pretty sure 2 of the BU stops are gone to make room for the new bike lanes. Can't wait for a news piece on how evil cyclists are even attacking the T now
Plan for station consolidation predated any of the plans for the new bike lanes.
For instance, October 2014 discussion of station consolidation http://www.bostonmagazine.com/news/blog/2014/10/16/mbta-green-line-stops-eliminate-discussion/
Announcement of bike infrastructure did not occur until March 2015.