Chronologically it does, but - with the exception of Chromedome having a webcam chat with the Masterforce Autobots along the lines of "sry GTG fighting Decepticons BRB" and then sending them some stuff for their acquisitions thread, and then Scorponok getting a new body - Masterforce is pretty much its own self-contained story. Which is part of its brilliance - it takes Transformers in a totally new direction and creates its own mythos.