JLCPCB has started the production of the PCBs. They passed the initial approval process. I'm not sure if that process is automated or not. According to the DFM analysis, it looks like I had my whole board rotated. Not just footprints being rotated, but the entire board?
The DFM analysis noted the following error "Cannot find this Pad in your PCB" for U1 and U6. I'm guessing this means that it could not determine pin 1, but in both cases the parts are correctly placed. Some parts that are on the assembly list don't show up in this rendering namely the switches and the common mode filter. I've emailed to find out the details on that.