This may not be the answer you want, but, you can cleave a window through the new door (then merge all the sectors back into one). You'd need to use a custom door cog that didn't change the flags of the adjoin surfaces for the sector that the door is in. I'm doing that for my own door 3DO's.
I don't know if you can have a transparant window MAT on a 3DO. I'd also like to know if it's possible to make a 3DO that uses see-through MATs (like the kind of MAT for a slash grate). I did realize you can animate a mat on a 3DO, such as a door, after seeing the blinking red light on the manual sequencer charge. You can use the regular mat animating cog and specify the name of the mat (but this animates the mat anywhere it appears).
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