I'll take a stab...
1) While Sullivan might have had some or any doubt in March 2018, his Memorandum of Opinion on December 2019 (linked by sr21 above) is pretty clear about what he thinks on materiality. Furthermore, it applies that to both the FBI and FARA violations admissions.
2) The notion that "Van Grack used the “magic words”, Judge Sullivan repeated the “magic words”, and viola, Gen. Flynn was guilty" glosses over the fact that Flynn was guilty because he pleaded to be. He was asked a mul ude of times if he understood what he was agreeing to by the judge, to which he replied yes every time. That's how pleas normally work.
3) "in Fokker Services the Circuit Court said that charging decisions by the Executive Branch are not subject to second-guessing by the Judiciary under any form of “discretionary review” authority conferred by any statute or rule of procedure."... the problem with this statement is that there's no discretionary review going on here. Sullivan isn't conducting a review, he simply hasn't ruled yet on the motion. That argument makes sense if he denied the motion, but he hasn't done so yet, which is why the writ is premature.
4) Another analysis that doesn't touch on the issue that Flynn not only admitted to lying to the FBI, but also to the DOJ multiple times wrt FARA violations. All charges are part of his plea agreement. The DOJ moved to dismiss on all charges even though they only presented support for that on the materiality for the FBI charge. This is, at the very least, extremely sloppy and a big reason why Judge Sullivan is probably uneasy with just granting the motion. It also unfortunately opens the door for judicial sanctions against Flynn, unless the DOJ supplements their motion (which they could do, they're the DOJ after all) explaining why there was no materiality on the lies about the FARA violation(s).