The larger DC-DC converters are not as cost sensitive as a raspberry pi product; they tend to be used in low volume industrial/scientific/medical devices and might cost £70 each. When you consider that they are also mostly inductor by area, and factor in the additional complexity of manufacturing a multiple-pcb assembly, it's also not worth it.
IIRC there are also some larger PCBs in that video; for those it's possible that they already had enough layers for routing signals that it was easy to integrate the transformer core directly.
Another factor I haven't seen mentioned is the manufacturing complexity. It looks like the transformer could be placed by a normal pick and place machine, while assembling a transformer around a PCB would be more of a specialised or manual process. I suspect that might be the real reason, as the transformer PCB doesn't look like it has that many layers.