I won't get to the revised via layout until next week, but I could make a PR for the other changes soon (tonight or tomorrow). That would be moving the logo, rotating the boards, going to 4 layers, removing soldermask, fixes to the 1x0p5 pad frame and removing vias from between die and pads on the 1x0p5 CoB only.
I'll leave panelisation to Andrew. When do you need to order the boards?