If I was you I wouldn't get too caught up on the casing. I'd simply mount the Zero on bottom of the casing, fabricate a plexiglas holder giving you maximum access to the GPIO pins for use at a later stage
If as I suspect Authinx dismiss your idea you always have the mod available to current and future WM100 owners should they choose to go that route. They can then decide what platform they require to run it on.
I've not got a mod for the WM100 that would require more knowledge and expertise then I have. It will take a community effort to develop that.
A SBC inside a WM100 was pitched to Authinx for a Pro version which I believe the factory shot down,
for reasons I wasn't told. I've not yet heard many details of what is/was planed for a Pro version.
In my opinion it isn't looking much like a pro version but I've been wrong before.
Current issues with the WM100 software may put all that on hold.
The zero W in the CM15A doesn't limit exposure to the GPIO pins I can still access them by sliding/removing the battery cover.
Also Authinx hasn't totally dismissed the idea of a SBC inside a CM15 though I wouldn't hold your breath for it.
I'm still working on the SBC options and connections for the CM15, I also want a cleaner look then my proof of concept.