I've been researching something similar--attempting to figure out if any other system 3-7 backboxes/insert boards will work for a Williams Pharaoh. The parts manual seems to indicate one backglass design (which then says to specify which game it's for), and one backbox/insert board design as well.
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I don't know if that's enough proof to say it will work for sure, but that's the way I'm approaching it so far. As you've noted, the displays seem to always be in the same spots, so it seems likely it should line up. Some alterations will have to be made regardless, but I think the core parts should be workable.

Have you come up with a backbox wiring harness for your game yet?

Tri zone is 6 digit, 7 digit displays are needed for Cosmic Gunfight, could get a LED 7 digit replacement set and new ribbon cables that are needed between the displays and display driver as display led kit don't include them.
The insert door displays will need to be modified to align 7 digit displays and credit match display in the backglass windows, the display mounting hardware could be re used to re locate the displays.

Backglass to insert clearances, wire harness to cpu to display driver board and backbox should be the same.

If the display windows in the BG are in the same place, the upper 2 studs in each 6 digit display correspond to the upper 2 on the 7 digit displays. The one that's a PITA to locate is the credit display, but it can be done. All the people that did the 6-7 digit conversions on the system 6 games had to do it. I forget what trick I used for this.... likely something involving double stick tape or make velcro? Just to locate the display, not permanent mount.

found it on oliver's page:
http://www.pinball4you.ch/okaegi/pro_d7f.html

Midway down he calls out how to mount the credit display properly.