While Judge Ellis ripped Muellers team a new one in court, I think he will ultimately rule against Manafort.
(1) Rosenstein's initial memo authorized Mueller to investigate "any matters that arose or may arise directly from that investigation."
(2) Rosenstein's follow up memo states the Manafort allegations "were within the scope of the investigation at the time of [his] appointment and are within tthe scope of the order."
(3) Further, it states Mueller "therefore [has] the authority to continue and complete the investigation of those matters..."
In sum, the DOJ expressly directed and authorized Mueller to investigate any potential crimes that he uncovered regarding Manafort during the course of his investigation.
I understand and respect Judge Ellis' concerns regarding "unfettered" power, but I believe he was largely playing devils advocate and posturing. Once he reviews the memos and contemplates the scenario, I suspect he'll agree that Mueller certainly did have the rightful authority to investigate any additional potential crimes he uncovered during the investigation whether they were directly tied to Russian "collusion" or not.
This is akin to a WARRENTED search of one's property for evidence of one crime and then stumbling upon evidence of another unrelated crime. It is legal, proper and - in the case of Mueller v. Manafort - EXPRESSLY AUTHORIZED by the DOJ.
Should Mueller lose, an appeal is in order. But, I doubt that will be necessary.
It's worth noting that Ellis is apparently not contemplating throwing out the charges, rather, he raised issues about venue. If anything, he would likely only reassign the casse to a different prosecutorial branch within the DOJ. Manaforts not performing a Houdini act here folks.