While I'm not fluent in legalese, it seems like the Cease and Desist letter boiled down to saying that the B9C vat assembly and mechanism are covered under pending patent that Michael filed, giving him the right to tell Josh of Makerjuice that he isn't allowed to make them. But, because MJ resin isn't specific to B9C the way the vat is, he's allowed to say his resin is compatible with B9C without violating copyright.
As to why he's fine with the aluminum vats, maybe that's because it's not a straight clone? Just guessing on that part.
In a larger context, there's been a lot of talk lately on what constitutes "open source". Open source hardware and software are really great, and have driven this community, but there's also a place for patents. However, by definition, to call a patented device "open source", even if you're sharing the design files, is a misnomer. For example, Microsoft regularly shares the source code for some of their project, while retaining all rights, which is essentially what Michael is doing with the hardware side of B9C. That's not a criticism, as there's a place for both open source and proprietary design...it's just an observation.