It looks as if the talk about Clover opening a cafe on Newbury Street is true after all. In 2012, the Boston Business Journal reported that Clover had leased a 275-square-foot sidewalk space from the city behind the Hynes MBTA station (354 Newbury Street).
Much more recently, a small Clover sign popped up at that location, and a new job posting on the company's website mentions Newbury. There's also a job posting mentioning the "first store in Boston," although that is likely to be a full restaurant, not the tiny Newbury Street spot, as the description mentions "a team of up to 45 employees." So stay tuned for upcoming Boston Clover(s).