What control software are you using for your cnc machine?
I use mach3 which allows you to set up work co ordinates for doing repeat work. I have made most of my jigs from ply mainly because I was worried that over time mdf would warp/swell with moisture. My unit isn't the driest warmest place in the winter
The jigs were cut on the cnc & have dowel holes which fit into the spoilboard, means I can put the jig on the table in exactly the same place every time & then using the right work co ordinates my x & y zero is always set to the same place.
I have cut my pockets all the way through the ply but they probably don't need to be that deep, I wouldn't think 1/8" would be deep enough though, mine are deep enough that they aid holding the part as well as aligning it, with an 1/8" pocket you would be relying on just the tape for hold down unless you intend using clamps as well which means you cant machine the whole surface of your part
I use the same file all the time, I just open it, alter the material thickness & then recalculate the toolpaths, you will get a message about recalculating toolpaths if you alter anything on the material set up page which is handy as it means you can't forget to do it
If I need to change any of the artwork I will do that & then save the file as a different name & keep the original as it was. I set my z axis from the top of the material because that is just the way I have always worked but you could set it from the table/material bottom so your z 0 would always be in the same place regardless of material thickness.
As with most things it depends on what you are doing, it will take time to set up the files & cut your jig so for a one off it might not be worth spending the time to do it but if this is something you do fairly regularly then once you have done the initial work every other one is pretty quick to do