This order is nothing exceptional.
You have a 'suggestions' from the judge (he could blow everything up and just direct what will be filed and when - he appears to be open to getting everything covered that needs to be addressed and adjust course as necessary). You have motions from the opposing sides, which are essentially responses (one says bad, the other says good). The judge is saying file what is essentially a reply. Nothing radical there. He also writes that the parties will discuss whether more is require at the 8/12 status conference.
Federal courts routinely use magistrate judges to work settlement conferences. Principals with the authority to settle actions are ordered to attend hearings, so that the courts avoid the "I will have to check with my boss" from attorneys. That can make a productive conference unproductive if an attorney lacks authority to agree to a deal. This occurs in the typical federal cases, as settlement agreements are always the peaceful way out for a court (and generally represent the easiest way to end a case).
I would expect the judge may push the NFL to consider a "status quo" injunction on Brady's suspension at that conference until the issues are resolved here. If the NFL's true target is Brady, and the NFL is playing checkers, then it would likely not agree. If the NFL's true target is a judicial interpretation of the CBA that validates the authority exercised in Brady's case (bad for all targets of discipline in the future) and avoids future federal cases (chess), then it might agree to that "status quo" in order to curry favor with the court and demonstrate how reasonable the NFL is in this case.