Maybe you could get Jscherb involved in a design.
OK, I'll bite...
Making fender boxes in fiberglass would be fairly straightforward. I wouldn't mess with 3d printing a mold master (or "plug" as some people call it) for these because it would be a challenge to exactly match the curve of the inner fenders starting from scratch with CAD unless you've got a 3d scanner. I would make the pattern for the inner fender curve right on the Jeep. I did a similar thing when I was making the front and rear flat fenders for the JK/JKU. I'll explain the process, but first a final photo of the fenders:
Unlike the TJ with its flat sides, the JKs fenders mount in a very contoured recess in the body. This is the recess for a rear fender:
It would have been very difficult to recreate that in CAD from scratch for 3d printing, so I molded a pattern right on the Jeep.
The first step was masking off the area not to be molded:
Then I applied mold release and sprayed gelcoat and built up layers of fiberglass mat+resin:
Once the fiberglass cured, I popped the rough flanges off the Jeep and trimmed them. I now had perfectly fitting mounting flanges for the fenders. BTW the photo above that shows the body-side recess before masking - I took that photo after I molded the flanges and removed the masking to show that parts can be molded right on the body with no damage to the body.
I'll switch to the front fenders now because I don't have a photo of this step for the rears. I bolted the flange to the body and built mockup fenders out of cardboard. This allowed me to perfect the final look and the cardboard provided cutting templates for the next step, which was to build the rest of the mold master out of MDF - they're flat fenders so flat, smooth MDF was perfect for this task, and would be perfect for building the body of the fender box in question.
Once I had the MDF masters done with the fiberglass flanges epoxied to the back of them, I put a nice finish on them, made molds, and molded the final fenders in those molds.
The same process can be done to make a perfectly fitting inner fender box. Mold the profile of the inner fender like I did with the fender flanges, use cardboard to build the box on top of that profile, use the cardboard as templates to make the box in MDF, put a nice finish on the MDF and make a mold. Then mold as many fender boxes as you like using that mold.
For this post I've skipped a few of the finer points that would be required for a fender box and the mold making process but if anyone is going to do this project I can provide more guidance.
I can't do the project myself because I don't have a TJ, I've only got an LJ.