I am making a custom shower, planning to cut my own stone slabs from stones found in my area. They will be granite, quartz, some others, that I cut with my own saw. I'm wondering how to attach the stones to backerboard so that the assembly is waterproof. The pan will be thin concrete over backerboard as well. Considering attaching expanded metal to backerboard with a 1-2mm gap and then using standard thinset buttered to back of stone then setting to wall. But then how to waterproof the assembly?
What you are doing sounds like you could simply use modified thinset. If the tile will be uniform, or perhaps not you could use tile setters shims to create the joints and then use sanded grout to fill the joints. You could use epoxy grout, I never have in a shower stall, but I am sure it would work.
As far as waterproofing goes starting with the floor pan, I have never seen backer board used on the floor. I have seen ready made bases that will accept tile, I have set a sloped sub base and installed PVC liner with a dry pack mud bed over that with cement board on the walls only, and then painted the walls and floor with a roll on membrane. After that, tile is set and grouted.
Normally the stone is applied directly to the backer board once the pieces are set a grout is used between the stones (today I would recommend epoxy grout). After grout a sealer can be used , I have done a couple jobs like this and do not recommend for a shower area. Even if well sealed natural stone picks up the soap scum and can be a pita to clean. I did a job for a guy that cut his stones , I thought it looked good and was remodeling a bath at my own home so I used my tile saw and did that shower it looked great, about a month later my wife was complaining about it, by 2 months I had to remove it and tile it. Several months later the customer called and asked how much to demo and replace he had the same issue but he had some fungus growing.
I have done other stone work and it was fine but in the shower it was hard to clean.