What gear this was done with is inconsequential compared to the idea and the amount of effort it must have taken to coordinate that whole thing. That’s what really impressed me.
Watch it frame-by-frame. You should be able to figure it out. A lot of times what you think you see is not what’s really there or is a lot simpler than it looks when it’s flying by.
Some effects are built specifically for transitions between full-screen video and will not work with titles or other keyed elements such as a logo. Some of them can be modified in Motion to work correctly with titles by turning off the A or B layer.
I have run into this. The only thing that worked was to make a new document in Photoshop and copy the layers into it from the original document. According to the graphic artist I was working with she has seen this before in some of her graphics apps.