I think McKnight did play some of his best football as a Dolphin the final few games last year. However, I think two things push Thompson in as the starter.
First, it wasn't too long ago that McKnight was considered overpaid and under-achieving by the coaching staff. Heck, we signed Cris Carter out of a television studio and started him two weeks later because we didn't think McKnight was a solid #2 WR. So while the CS has praised McKnight publically in recent weeks, I am not sure how genuine the praise actually is. I think they might be trying to ward off negative comments in the press and public regarding the lack of signing or drafting a big-name WR. The FO also didn't really know exactly what they had in Thompson until seeing him on the field at mini-camp with the rest of the team. The McKnight praise also could have been pre-emptive in case Thompson did not pan out the way they hoped and McKnight had to start.
Second, I think that Chambers has been more comfortable and effective when he runs more deep patterns while a possession receiver plays the other WR (like Gadsden). Chambers struggled a bit last year when asked to run the possession routes. Thompson can play the possession receiver better than McKnight. When we go to a 3-wide formation, McKnight can come in and still play on the outside. The CS has mentioned that they want to move Chambers around in the 3-wide formation, leaving McKnight in his most natural, wide position in the formation.