The Bezel-less popup can be toggled by clicking on the top of the PFD in the 3D cockpit, near the logo on the bezel. Regarding size saving and positioning, the logic for that goes through the RealSimGear plugin with their hardware. Without that, positions can be saved manually, editing the popups.cfg file for the x and y locations, coordinates are pixels measured from bottom left of the OS primary monitor.
Regarding PFD customization, it isn't on our scope currently, but we will look into it in the future.