Al, I'm no expert by any means. I cut my closed cell foam all the way to the edge of the panel board. My panel board was from 1/8" non-wood panels bought as 4'X8' @ home depot. The panels I used where smooth painted on one side and bare on the other. Which either side you use, you want to rough up that surface a bit so your glue holds tight. I cut my panels nearly all the way to the edge of the door. Your probably good using 1/8" from the edge. If your using the push through nylon panel clips, the holes need to be pre-cut and verified for fitment before covering the panel.
I'm not sure I know what your talking about rubber seals. The door panel shouldn't interfere with any door seals/weatherstripping. Your windlace spoken of earlier should touch your door panel when the door in closed. Have your windlace already installed before doing the rear interior panels. They (rear panels) will butt up to the very edge of the windlace to give a nice finished look. ~robert